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(-) Description

Title :  2.25A RESOLUTION STRUCTURE OF TRANSMISSIBLE GASTROENTERITIS VIRUS PROTEASE CONTAINING A COVALENTLY BOUND DIPEPTIDYL INHIBITOR
 
Authors :  S. Lovell, K. P. Battaile, Y. Kim, K. -C. Tiew, S. R. Mandadapu, K. R. Alli W. C. Groutas, K. -O. Chang
Date :  10 May 12  (Deposition) - 05 Sep 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Protease, Antiviral Inhibitors, Dipeptidyl Inhibitor, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, S. Lovell, K. C. Tiew, S. R. Mandadapu, K. R. Alliston, K. P. Battaile, W. C. Groutas, K. O. Chang
Broad-Spectrum Antivirals Against 3C Or 3C-Like Proteases O Picornaviruses, Noroviruses, And Coronaviruses.
J. Virol. V. 86 11754 2012
PubMed-ID: 22915796  |  Reference-DOI: 10.1128/JVI.01348-12

(-) Compounds

Molecule 1 - 3C-LIKE PROTEINASE
    Chains: A, B, C, D
    EC Number: 3.4.22.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28(+)
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: 1A
    Organism Common: TGEV
    Organism Scientific: PORCINE TRANSMISSIBLE GASTROENTERITIS CORONAVIRUS
    Organism Taxid: 11151
    Strain: PURDUE
    Synonym: 3CL-PRO, 3CLP, M-PRO, NSP5, P34

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1K364Ligand/Ion(1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
2PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1K361Ligand/Ion(1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
2PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1K361Ligand/Ion(1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
2PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1K361Ligand/Ion(1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
2PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1K361Ligand/Ion(1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
2PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:41 , PHE A:139 , ILE A:140 , GLY A:142 , THR A:143 , CYS A:144 , HIS A:162 , HIS A:163 , LEU A:164 , GLU A:165 , HIS A:171 , GLN A:187 , HOH A:513BINDING SITE FOR RESIDUE K36 A 401
2AC2SOFTWAREHIS B:41 , PHE B:139 , ILE B:140 , GLY B:142 , THR B:143 , CYS B:144 , HIS B:162 , HIS B:163 , LEU B:164 , GLU B:165 , HIS B:171 , GLN B:187 , PRO B:188 , HOH B:548BINDING SITE FOR RESIDUE K36 B 401
3AC3SOFTWARETHR C:47 , ILE C:51 , PHE C:139 , ILE C:140 , GLY C:142 , THR C:143 , CYS C:144 , HIS C:162 , HIS C:163 , LEU C:164 , GLU C:165 , HIS C:171 , GLN C:187 , HOH C:523BINDING SITE FOR RESIDUE K36 C 401
4AC4SOFTWAREPHE D:139 , ILE D:140 , ALA D:141 , THR D:143 , CYS D:144 , HIS D:162 , HIS D:163 , LEU D:164 , GLU D:165 , HIS D:171 , GLN D:187 , PRO D:188BINDING SITE FOR RESIDUE K36 D 401
5AC5SOFTWAREARG A:19 , SER A:21 , ARG D:267 , LYS D:270 , HOH D:502 , HOH D:519BINDING SITE FOR RESIDUE PG4 D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F49)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F49)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F49)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F49)

(-) Exons   (0, 0)

(no "Exon" information available for 4F49)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4f49a_ A: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhh.eeeee..eee.eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f49 A   0 HSGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV 299
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299


Chain B from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4f49b_ B: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee.........eee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f49 B   1 SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYG 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 ||    251       261       271       281       291       
                                                                                                                                                                                                                                                                           242|                                                      
                                                                                                                                                                                                                                                                            244                                                      


Chain C from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4f49c_ C: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhhhhhh.eeeee..ee..eeeeeee..eeeeee..........ee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f49 C   0 HSGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV 299
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299


Chain D from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4f49d_ D: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhh.eeeeee..eeeeeeee..eeeee.hhhh.......hhhhhhhh.hhhhheee......eeeeeee..eeeeee.........eee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee.....hhhhh..............hhhhhhhhhhhhhhh...........hhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f49 D   0 HSGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGV 299
                                     9        19        29        39        49        59        69||      80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         
                                                                                                 70|                                                                                                                                                                                                                                   
                                                                                                  72
   Legend:   → Mismatch (orange background)
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  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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F49)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F49)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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        R1A_CVPPU | P0C6V2: 1lvo 1p9u 2amp 3mp2 3zbd

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