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(-) Description

Title :  STRUCTURE OF CORONAVIRUS MAIN PROTEINASE REVEALS COMBINATION OF A CHYMOTRYPSIN FOLD WITH AN EXTRA ALPHA-HELICAL DOMAIN
 
Authors :  K. Anand, G. J. Palm, J. R. Mesters, S. G. Siddell, J. Ziebuhr, R. Hilgenfeld
Date :  29 May 02  (Deposition) - 17 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  3C Like, Corona, Proteinase, Chymotrypsin, Cysteine Histidine Dyad, Beta Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Anand, G. J. Palm, J. R. Mesters, S. G. Siddell, J. Ziebuhr, R. Hilgenfeld
Structure Of Coronavirus Main Proteinase Reveals Combination Of A Chymotrypsin Fold With An Extra Alpha-Helical Domain.
Embo J. V. 21 3213 2002
PubMed-ID: 12093723  |  Reference-DOI: 10.1093/EMBOJ/CDF327
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPLICASE, HYDROLASE DOMAIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2
    Expression System Strain: TB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2879-3180
    Gene: ORF1A
    Organism Scientific: TRANSMISSIBLE GASTROENTERITIS VIRUS
    Organism Taxid: 11149

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 42)

Asymmetric Unit (3, 42)
No.NameCountTypeFull Name
1DIO9Ligand/Ion1,4-DIETHYLENE DIOXIDE
2MRD6Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3SO427Ligand/IonSULFATE ION
Biological Unit 1 (3, 15)
No.NameCountTypeFull Name
1DIO4Ligand/Ion1,4-DIETHYLENE DIOXIDE
2MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3SO49Ligand/IonSULFATE ION
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
2MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3SO410Ligand/IonSULFATE ION
Biological Unit 3 (3, 13)
No.NameCountTypeFull Name
1DIO3Ligand/Ion1,4-DIETHYLENE DIOXIDE
2MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3SO48Ligand/IonSULFATE ION
Biological Unit 4 (3, 15)
No.NameCountTypeFull Name
1DIO4Ligand/Ion1,4-DIETHYLENE DIOXIDE
2MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3SO49Ligand/IonSULFATE ION

(-) Sites  (41, 41)

Asymmetric Unit (41, 41)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU C:179BINDING SITE FOR RESIDUE SO4 C 3001
02AC2SOFTWAREARG C:130 , ASN C:196BINDING SITE FOR RESIDUE SO4 C 3002
03AC3SOFTWAREASN A:168 , LEU A:192 , GLU A:193 , GLY A:194 , HOH A:4029BINDING SITE FOR RESIDUE SO4 A 3003
04AC4SOFTWAREARG A:130 , LYS A:136 , ASN A:196 , HOH A:4135BINDING SITE FOR RESIDUE SO4 A 3004
05AC5SOFTWAREASN C:168 , LEU C:192 , GLU C:193 , GLY C:194 , HOH C:4077BINDING SITE FOR RESIDUE SO4 C 3005
06AC6SOFTWAREASN B:168 , GLU B:193 , GLY B:194 , HOH B:4075 , HOH B:4158BINDING SITE FOR RESIDUE SO4 B 3006
07AC7SOFTWAREHOH B:4178 , ASN E:168 , LEU E:192 , GLU E:193 , GLY E:194BINDING SITE FOR RESIDUE SO4 E 3007
08AC8SOFTWAREARG D:130 , ASN D:196 , HOH D:4083BINDING SITE FOR RESIDUE SO4 D 3008
09AC9SOFTWAREARG E:130 , HOH E:4100 , HOH E:4184 , HOH E:4210BINDING SITE FOR RESIDUE SO4 E 3009
10BC1SOFTWAREASN F:168 , LEU F:192 , GLU F:193 , GLY F:194BINDING SITE FOR RESIDUE SO4 F 3010
11BC2SOFTWAREGLY A:214 , GLU A:215 , ARG A:216 , TRP A:217BINDING SITE FOR RESIDUE SO4 A 3011
12BC3SOFTWAREASN D:168 , LEU D:192 , GLU D:193 , GLY D:194 , HOH D:4026BINDING SITE FOR RESIDUE SO4 D 3012
13BC4SOFTWAREARG E:275 , THR E:276 , HOH E:4094BINDING SITE FOR RESIDUE SO4 E 3013
14BC5SOFTWAREARG C:275 , THR C:276BINDING SITE FOR RESIDUE SO4 C 3015
15BC6SOFTWAREGLY D:214 , ARG D:216 , TRP D:217 , HOH D:4168BINDING SITE FOR RESIDUE SO4 D 3016
16BC7SOFTWAREARG D:275 , THR D:276BINDING SITE FOR RESIDUE SO4 D 3017
17BC8SOFTWAREVAL E:60 , ARG E:61 , LEU E:62 , HIS E:63BINDING SITE FOR RESIDUE SO4 E 3018
18BC9SOFTWAREARG F:216 , TRP F:217 , DIO F:2003BINDING SITE FOR RESIDUE SO4 F 3019
19CC1SOFTWARELYS B:82 , PHE B:102 , PHE B:176BINDING SITE FOR RESIDUE SO4 B 3020
20CC2SOFTWAREARG C:294 , ALA D:115 , SER D:123BINDING SITE FOR RESIDUE SO4 D 3021
21CC3SOFTWARELYS A:103 , SER A:104BINDING SITE FOR RESIDUE SO4 A 3022
22CC4SOFTWAREGLY C:214 , GLU C:215 , ARG C:216 , TRP C:217 , ARG C:275 , HOH C:4035BINDING SITE FOR RESIDUE SO4 C 3023
23CC5SOFTWAREARG F:61 , LEU F:62 , HIS F:63BINDING SITE FOR RESIDUE SO4 F 3024
24CC6SOFTWAREARG F:130 , LYS F:136 , ASN F:196BINDING SITE FOR RESIDUE SO4 F 3025
25CC7SOFTWAREARG B:19 , SER B:21 , HOH B:4070 , HOH B:4116BINDING SITE FOR RESIDUE SO4 B 3026
26CC8SOFTWAREARG A:19 , SER A:21 , VAL A:26BINDING SITE FOR RESIDUE SO4 A 3027
27CC9SOFTWAREGLY B:273 , ARG E:216 , TRP E:217 , HOH E:4063 , HOH E:4132 , HOH E:4229 , HOH E:4230BINDING SITE FOR RESIDUE DIO E 2001
28DC1SOFTWARESER E:123 , HOH E:4185 , MET F:6BINDING SITE FOR RESIDUE DIO E 2002
29DC2SOFTWAREGLY F:274 , ARG F:275 , THR F:276 , SO4 F:3019BINDING SITE FOR RESIDUE DIO F 2003
30DC3SOFTWAREASN A:112 , GLU A:291BINDING SITE FOR RESIDUE DIO A 2004
31DC4SOFTWARESER A:131 , GLN A:132 , GLY A:133BINDING SITE FOR RESIDUE DIO A 2005
32DC5SOFTWAREGLY A:122 , SER A:123 , HOH A:4112BINDING SITE FOR RESIDUE DIO A 2006
33DC6SOFTWAREPHE B:139 , CYS B:144 , HIS B:162 , GLU B:165BINDING SITE FOR RESIDUE DIO B 2007
34DC7SOFTWARESER C:223 , MET C:224 , SER C:225 , SER C:228BINDING SITE FOR RESIDUE DIO C 2008
35DC8SOFTWARELYS C:136 , HOH C:4124 , GLY D:2 , ASN D:213BINDING SITE FOR RESIDUE DIO C 2009
36DC9SOFTWAREHIS A:41 , HIS A:163 , LEU A:164 , GLN A:187 , PRO A:188BINDING SITE FOR RESIDUE MRD A 4001
37EC1SOFTWAREHIS B:41 , THR B:47 , ILE B:51 , TYR B:53 , LEU B:164 , ASP B:186 , HOH B:4192BINDING SITE FOR RESIDUE MRD B 4002
38EC2SOFTWAREHIS C:41 , THR C:47 , ILE C:51 , TYR C:53 , LEU C:164 , ASP C:186BINDING SITE FOR RESIDUE MRD C 4003
39EC3SOFTWAREHIS D:41 , ILE D:51 , TYR D:53 , LEU D:164 , ASP D:186 , GLN D:187 , PRO D:188BINDING SITE FOR RESIDUE MRD D 4004
40EC4SOFTWAREHIS E:41 , THR E:47 , HIS E:163 , LEU E:164 , ASP E:186 , GLN E:187 , HOH E:4045BINDING SITE FOR RESIDUE MRD E 4005
41EC5SOFTWAREHIS F:41 , THR F:47 , ASP F:186 , GLN F:187 , PRO F:188BINDING SITE FOR RESIDUE MRD F 4006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LVO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LVO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LVO)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1M_PROPS51442 Coronavirus main protease (M-pro) domain profile.R1AB_CVPPU2879-3180
 
 
 
 
 		  6A:1-299
B:1-300
C:1-300
D:1-301
E:1-299
F:1-299
R1A_CVPPU2879-3180
 
 
 
 
 		  6A:1-299
B:1-300
C:1-300
D:1-301
E:1-299
F:1-299
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1M_PROPS51442 Coronavirus main protease (M-pro) domain profile.R1AB_CVPPU2879-3180
 
 
 
 
 		  2A:1-299
B:1-300
-
-
-
-
R1A_CVPPU2879-3180
 
 
 
 
 		  2A:1-299
B:1-300
-
-
-
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1M_PROPS51442 Coronavirus main protease (M-pro) domain profile.R1AB_CVPPU2879-3180
 
 
 
 
 		  2-
-
C:1-300
D:1-301
-
-
R1A_CVPPU2879-3180
 
 
 
 
 		  2-
-
C:1-300
D:1-301
-
-
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1M_PROPS51442 Coronavirus main protease (M-pro) domain profile.R1AB_CVPPU2879-3180
 
 
 
 
 		  2-
-
-
-
E:1-299
F:1-299
R1A_CVPPU2879-3180
 
 
 
 
 		  2-
-
-
-
E:1-299
F:1-299
Biological Unit 4 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1M_PROPS51442 Coronavirus main protease (M-pro) domain profile.R1AB_CVPPU2879-3180
 
 
 
 
 		  6A:1-299
B:1-300
C:1-300
D:1-301
E:1-299
F:1-299
R1A_CVPPU2879-3180
 
 
 
 
 		  6A:1-299
B:1-300
C:1-300
D:1-301
E:1-299
F:1-299

(-) Exons   (0, 0)

(no "Exon" information available for 1LVO)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:299
 aligned with R1AB_CVPPU | P0C6Y5 from UniProtKB/Swiss-Prot  Length:6684

    Alignment length:299
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168         
          R1AB_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV 3177
               SCOP domains d1lvoa_ A: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------1lvoA01 A:14-97 Trypsin-like serine proteases                                       1lvoA02 A:98-185 Trypsin-like serine proteases                                          -----------1lvoA03 A:197-299 main proteinase (3clpro) structure, domain 3                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE M_PRO  PDB: A:1-299 UniProt: 2879-3180                                                                                                                                                                                                                                                                      PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvo A    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV  299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain A from PDB  Type:PROTEIN  Length:299
 aligned with R1A_CVPPU | P0C6V2 from UniProtKB/Swiss-Prot  Length:4017

    Alignment length:299
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168         
           R1A_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV 3177
               SCOP domains d1lvoa_ A: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------1lvoA01 A:14-97 Trypsin-like serine proteases                                       1lvoA02 A:98-185 Trypsin-like serine proteases                                          -----------1lvoA03 A:197-299 main proteinase (3clpro) structure, domain 3                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) M_PRO  PDB: A:1-299 UniProt: 2879-3180                                                                                                                                                                                                                                                                      PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvo A    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV  299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with R1AB_CVPPU | P0C6Y5 from UniProtKB/Swiss-Prot  Length:6684

    Alignment length:300
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168      3178
          R1AB_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVN 3178
               SCOP domains d1lvob_ B: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------1lvoB01 B:14-97 Trypsin-like serine proteases                                       1lvoB02 B:98-185 Trypsin-like serine proteases                                          -----------1lvoB03 B:197-299 main proteinase (3clpro) structure, domain 3                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhh.eeee.......eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE M_PRO  PDB: B:1-300 UniProt: 2879-3180                                                                                                                                                                                                                                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1lvo B    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVN  300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with R1A_CVPPU | P0C6V2 from UniProtKB/Swiss-Prot  Length:4017

    Alignment length:300
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168      3178
           R1A_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVN 3178
               SCOP domains d1lvob_ B: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------1lvoB01 B:14-97 Trypsin-like serine proteases                                       1lvoB02 B:98-185 Trypsin-like serine proteases                                          -----------1lvoB03 B:197-299 main proteinase (3clpro) structure, domain 3                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhh.eeee.......eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) M_PRO  PDB: B:1-300 UniProt: 2879-3180                                                                                                                                                                                                                                                                       PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1lvo B    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVN  300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300


Chain C from PDB  Type:PROTEIN  Length:300
 aligned with R1AB_CVPPU | P0C6Y5 from UniProtKB/Swiss-Prot  Length:6684

    Alignment length:300
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168      3178
          R1AB_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVN 3178
               SCOP domains d1lvoc_ C: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------1lvoC01 C:14-97 Trypsin-like serine proteases                                       1lvoC02 C:98-185 Trypsin-like serine proteases                                          -----------1lvoC03 C:197-299 main proteinase (3clpro) structure, domain 3                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhhhhhh................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE M_PRO  PDB: C:1-300 UniProt: 2879-3180                                                                                                                                                                                                                                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1lvo C    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVN  300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300


Chain C from PDB  Type:PROTEIN  Length:300
 aligned with R1A_CVPPU | P0C6V2 from UniProtKB/Swiss-Prot  Length:4017

    Alignment length:300
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168      3178
           R1A_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVN 3178
               SCOP domains d1lvoc_ C: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------1lvoC01 C:14-97 Trypsin-like serine proteases                                       1lvoC02 C:98-185 Trypsin-like serine proteases                                          -----------1lvoC03 C:197-299 main proteinase (3clpro) structure, domain 3                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhhhhhh................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) M_PRO  PDB: C:1-300 UniProt: 2879-3180                                                                                                                                                                                                                                                                       PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1lvo C    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVN  300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300


Chain D from PDB  Type:PROTEIN  Length:301
 aligned with R1AB_CVPPU | P0C6Y5 from UniProtKB/Swiss-Prot  Length:6684

    Alignment length:301
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168      3178 
          R1AB_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVNL 3179
               SCOP domains d1lvod_ D: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------1lvoD01 D:14-97 Trypsin-like serine proteases                                       1lvoD02 D:98-185 Trypsin-like serine proteases                                          -----------1lvoD03 D:197-299 main proteinase (3clpro) structure, domain 3                                         -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhhhhhhhheeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhhhhhhhhhh................hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE M_PRO  PDB: D:1-301 UniProt: 2879-3180                                                                                                                                                                                                                                                                        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvo D    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVNL  301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 


Chain D from PDB  Type:PROTEIN  Length:301
 aligned with R1A_CVPPU | P0C6V2 from UniProtKB/Swiss-Prot  Length:4017

    Alignment length:301
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168      3178 
           R1A_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVNL 3179
               SCOP domains d1lvod_ D: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------1lvoD01 D:14-97 Trypsin-like serine proteases                                       1lvoD02 D:98-185 Trypsin-like serine proteases                                          -----------1lvoD03 D:197-299 main proteinase (3clpro) structure, domain 3                                         -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhhhhhhhheeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhhhhhhhhhh................hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) M_PRO  PDB: D:1-301 UniProt: 2879-3180                                                                                                                                                                                                                                                                        PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvo D    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVNL  301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 


Chain E from PDB  Type:PROTEIN  Length:299
 aligned with R1AB_CVPPU | P0C6Y5 from UniProtKB/Swiss-Prot  Length:6684

    Alignment length:299
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168         
          R1AB_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV 3177
               SCOP domains d1lvoe_ E: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------1lvoE01 E:14-97 Trypsin-like serine proteases                                       1lvoE02 E:98-185 Trypsin-like serine proteases                                          -----------1lvoE03 E:197-299 main proteinase (3clpro) structure, domain 3                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhh..hhh.eeeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE M_PRO  PDB: E:1-299 UniProt: 2879-3180                                                                                                                                                                                                                                                                      PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvo E    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV  299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain E from PDB  Type:PROTEIN  Length:299
 aligned with R1A_CVPPU | P0C6V2 from UniProtKB/Swiss-Prot  Length:4017

    Alignment length:299
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168         
           R1A_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV 3177
               SCOP domains d1lvoe_ E: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------1lvoE01 E:14-97 Trypsin-like serine proteases                                       1lvoE02 E:98-185 Trypsin-like serine proteases                                          -----------1lvoE03 E:197-299 main proteinase (3clpro) structure, domain 3                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhh..hhh.eeeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) M_PRO  PDB: E:1-299 UniProt: 2879-3180                                                                                                                                                                                                                                                                      PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvo E    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV  299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain F from PDB  Type:PROTEIN  Length:299
 aligned with R1AB_CVPPU | P0C6Y5 from UniProtKB/Swiss-Prot  Length:6684

    Alignment length:299
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168         
          R1AB_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV 3177
               SCOP domains d1lvof_ F: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------1lvoF01 F:14-97 Trypsin-like serine proteases                                       1lvoF02 F:98-185 Trypsin-like serine proteases                                          -----------1lvoF03 F:197-299 main proteinase (3clpro) structure, domain 3                                          CATH domains
           Pfam domains (1) ----------------------------Peptidase_C30-1lvoF01 F:29-299                                                                                                                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) ----------------------------Peptidase_C30-1lvoF02 F:29-299                                                                                                                                                                                                                                                  Pfam domains (2)
           Pfam domains (3) ----------------------------Peptidase_C30-1lvoF03 F:29-299                                                                                                                                                                                                                                                  Pfam domains (3)
           Pfam domains (4) ----------------------------Peptidase_C30-1lvoF04 F:29-299                                                                                                                                                                                                                                                  Pfam domains (4)
           Pfam domains (5) ----------------------------Peptidase_C30-1lvoF05 F:29-299                                                                                                                                                                                                                                                  Pfam domains (5)
           Pfam domains (6) ----------------------------Peptidase_C30-1lvoF06 F:29-299                                                                                                                                                                                                                                                  Pfam domains (6)
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhh.............hhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhh........hhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE M_PRO  PDB: F:1-299 UniProt: 2879-3180                                                                                                                                                                                                                                                                      PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvo F    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV  299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain F from PDB  Type:PROTEIN  Length:299
 aligned with R1A_CVPPU | P0C6V2 from UniProtKB/Swiss-Prot  Length:4017

    Alignment length:299
                                  2888      2898      2908      2918      2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028      3038      3048      3058      3068      3078      3088      3098      3108      3118      3128      3138      3148      3158      3168         
           R1A_CVPPU   2879 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV 3177
               SCOP domains d1lvof_ F: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------1lvoF01 F:14-97 Trypsin-like serine proteases                                       1lvoF02 F:98-185 Trypsin-like serine proteases                                          -----------1lvoF03 F:197-299 main proteinase (3clpro) structure, domain 3                                          CATH domains
           Pfam domains (1) ----------------------------Peptidase_C30-1lvoF01 F:29-299                                                                                                                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) ----------------------------Peptidase_C30-1lvoF02 F:29-299                                                                                                                                                                                                                                                  Pfam domains (2)
           Pfam domains (3) ----------------------------Peptidase_C30-1lvoF03 F:29-299                                                                                                                                                                                                                                                  Pfam domains (3)
           Pfam domains (4) ----------------------------Peptidase_C30-1lvoF04 F:29-299                                                                                                                                                                                                                                                  Pfam domains (4)
           Pfam domains (5) ----------------------------Peptidase_C30-1lvoF05 F:29-299                                                                                                                                                                                                                                                  Pfam domains (5)
           Pfam domains (6) ----------------------------Peptidase_C30-1lvoF06 F:29-299                                                                                                                                                                                                                                                  Pfam domains (6)
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhh.............hhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhh........hhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) M_PRO  PDB: F:1-299 UniProt: 2879-3180                                                                                                                                                                                                                                                                      PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvo F    1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV  299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 18)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (40, 66)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (R1AB_CVPPU | P0C6Y5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016896    exoribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008242    omega peptidase activity    Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of alpha-carboxyl to alpha-amino groups).
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0039648    modulation by virus of host protein ubiquitination    Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039548    suppression by virus of host IRF3 activity    Any process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044172    host cell endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between host cell endoplasmic reticulum (ER) and the host Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi transport.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044220    host cell perinuclear region of cytoplasm    The host cell cytoplasm situated near, or occurring around, the host nucleus.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B,C,D,E,F   (R1A_CVPPU | P0C6V2)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008242    omega peptidase activity    Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of alpha-carboxyl to alpha-amino groups).
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0039648    modulation by virus of host protein ubiquitination    Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039548    suppression by virus of host IRF3 activity    Any process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044220    host cell perinuclear region of cytoplasm    The host cell cytoplasm situated near, or occurring around, the host nucleus.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  R1A_CVPPU | P0C6V2
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        R1AB_CVPPU | P0C6Y5: 1p9u 2amp
        R1A_CVPPU | P0C6V2: 1p9u 2amp 3mp2 3zbd 4f49

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LVO)