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(-) Description

Title :  LIGAND-BOUND STRUCTURE OF CAVALLY VIRUS 3CL PROTEASE
 
Authors :  M. Kanitz, A. Heine, W. E. Diederich
Date :  14 Jun 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,I,J,K
Biol. Unit 1:  A,B,I  (1x)
Biol. Unit 2:  C,D,J,K  (1x)
Keywords :  Protease, Mesonivirus, 3Cl, Peptide-Bound, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kanitz, S. Blanck, A. Heine, J. Ziebuhr, W. E. Diederich
The De-Novo And Ligand-Bound Structures Of Cavv 3Clpro Strongly Support The Existence Of A Non-Classical Dyad Across Different Nidovirus Families
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3CL PROTEASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2-(CAVV PP1A-1387-1700)
    Expression System Taxid: 562
    Expression System Variant: TB1
    Expression System Vector: PMAL-C2
    Expression System Vector Type: PLASMID
    Gene: PP1AB, CAVV_GP1
    Organism Scientific: CAVALLY VIRUS
    Organism Taxid: 1041929
 
Molecule 2 - BEZ-TYR-TYR-ASN-ECC PEPTIDE INHIBITOR
    Chains: I, J, K
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDIJK
Biological Unit 1 (1x): AB  I  
Biological Unit 2 (1x):   CD JK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
11PE3Ligand/IonPENTAETHYLENE GLYCOL
2BEZ3Mod. Amino AcidBENZOIC ACID
3ECC3Mod. Amino Acid(4S)-4-AMINO-5-HYDROXYPENTANAMIDE
4PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2BEZ1Mod. Amino AcidBENZOIC ACID
3ECC1Mod. Amino Acid(4S)-4-AMINO-5-HYDROXYPENTANAMIDE
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2BEZ2Mod. Amino AcidBENZOIC ACID
3ECC2Mod. Amino Acid(4S)-4-AMINO-5-HYDROXYPENTANAMIDE
4PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:143 , ASN A:208 , HIS A:226 , PRO A:227 , LEU A:228 , HOH A:542 , HOH A:556binding site for residue 1PE A 401
02AC2SOFTWAREASN B:208 , TYR B:224 , HIS B:226 , HOH B:520binding site for residue PGE B 401
03AC3SOFTWAREASN C:208 , HIS C:226 , PRO C:227 , HOH C:515 , HOH C:539binding site for residue 1PE C 402
04AC4SOFTWAREASN D:208 , TYR D:224 , HIS D:226 , HOH D:518binding site for residue 1PE D 401
05AC5SOFTWARESER A:1 , ALA A:2 , ALA A:3 , SER A:4 , PRO A:6 , SER A:7 , LEU A:34 , ARG A:35 , GLN A:46 , HIS A:48 , THR A:148 , VAL A:149 , GLY A:151 , ASP A:152 , GLY A:154 , GLY A:155 , HIS A:168 , CYS A:169 , HOH A:525 , THR B:136 , GLY B:137 , ASP B:145 , LYS B:147 , ARG C:28 , TYR I:3 , ASN I:4binding site for Ligand residues ECC I 5 through CYS A 153 bound to ASN I 4
06AC6SOFTWAREARG A:28 , SER C:1 , ALA C:2 , ALA C:3 , SER C:4 , PRO C:6 , SER C:7 , LEU C:34 , ARG C:35 , GLN C:46 , HIS C:48 , THR C:148 , VAL C:149 , GLY C:151 , ASP C:152 , GLY C:154 , GLY C:155 , HIS C:168 , CYS C:169 , THR D:136 , GLY D:137 , ASP D:145 , TYR J:3 , ASN J:4binding site for Ligand residues ECC J 5 through CYS C 153 bound to ASN J 4
07AC7SOFTWARETHR A:136 , GLY A:137 , ASP A:145 , LYS A:147 , SER B:1 , ALA B:2 , ALA B:3 , SER B:4 , PRO B:6 , SER B:7 , LEU B:34 , ARG B:35 , GLN B:46 , HIS B:48 , THR B:148 , VAL B:149 , PHE B:150 , GLY B:151 , ASP B:152 , GLY B:154 , GLY B:155 , HIS B:168 , CYS B:169 , HOH B:511 , TYR K:3 , ASN K:4binding site for Ligand residues ECC K 5 through CYS B 153 bound to ASN K 4
08AC8SOFTWAREGLY A:171 , SER A:172 , TYR A:215 , GLU A:218 , THR A:220 , TYR I:3binding site for Di-peptide BEZ I 1 and TYR I 2
09AC9SOFTWAREGLY C:171 , SER C:172 , TYR C:215 , GLU C:218 , THR C:219 , THR C:220 , VAL C:222 , TYR J:3binding site for Di-peptide BEZ J 1 and TYR J 2
10AD1SOFTWAREALA B:170 , SER B:172 , TYR B:215 , THR B:219 , THR B:220 , LYS B:221 , VAL B:222 , TYR K:3 , ASN K:4binding site for Di-peptide BEZ K 1 and TYR K 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LAK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LAK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LAK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LAK)

(-) Exons   (0, 0)

(no "Exon" information available for 5LAK)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh.eeeee....eeeee.eee..eeeee.hhhh.hhhhhhhhhhhhhhhh..........hhhhheee..eeeee..............hhhh.eeeeeeeeeeee..eeeeeeeeeeee...............eeee....eeeeeeeee........................eeeee.........hhhhhhhh...........hhhhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lak A   1 SAASNPSISHIVLEMPVAINPLIKYTTRTSVSSLRGAVVNGYIYIQRHLFGSKKQEFEACYNNGKGLLNCKNLERSKYDIDSAELIGTLIRIPLHDKHSIPHISIHPDPLSYNGPVTLYLSRYDTNKDVLCVHTGFMSEGHHDIKTVFGDCGGMLFDPKGRLLGLHCAGSDDVVFMDTTTGKSNIWTSYKLQHPSEIMITLNNEINLPNPANYDFETTKVVYQHPLRNVCATLETLQHLTNKTNAKLPYDSRLLSDFNITAEQYNQYGYYIDYNNFVNNFNRYTTTTIGTKSFETCIKYGLMD 305
                                    10        20        30        40        50        60        70        80        90       100       110       120    || 132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302   
                                                                                                                                                      125|                                                                                                                                                                                 
                                                                                                                                                       128                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhh.eee...eee.eee..eeeee.hhhh.hhhhhhhhhhhhhhhh..........hhhhheee..eeeee..............hhhh.eeeeeeeeeeee....eeeeeeeeeeee...............eeee....eeeeeeeee..................eeeee.........hhhhhhhhh..........hhhhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lak B   1 SAASNPSISHIVLEMPVAINPLIKYTSSLRGAVVNGYIYIQRHLFGSKKQEFEACYNNGKGLLNCKNLERSKYDIDSAELIGTLIRIPLHDKHSIPHISIHPDPLSYNGPVTLYLSRYDTELNKDVLCVHTGFMSEGHHDIKTVFGDCGGMLFDPKGRLLGLHCAGSDDVVFMDSNIWTSYKQHPSEIMITLNNEINLPNPANYDFETTKVVYQHPLRNVCATLETLQHLTNKTNAKLPYDSRLLSDFNITAEQYNQYGYYIDYNNFVNNFNRYTTTTIGTKSFETCIKYGLMD 305
                                    10        20     || 35        45        55        65        75        85        95       105       115       125       135       145       155       165       175   ||  190 ||    201       211       221       231       241       251       261       271       281       291       301    
                                                    26|                                                                                                                                                179|    192|                                                                                                               
                                                     32                                                                                                                                                 185     194                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh.eeeee....eeeee.eee..eeeee.hhhh.hhhhhhhhhhhhhhhh..........hhhhheee..eeeee..............hhhh.eeeeeeeeeeee..eeeeeeeeeeee...............eeee....eeeeeeeee........................eeeee.........hhhhh..............hhhhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lak C   1 SAASNPSISHIVLEMPVAINPLIKYTTRTSVSSLRGAVVNGYIYIQRHLFGSKKQEFEACYNNGKGLLNCKNLERSKYDIDSAELIGTLIRIPLHDKHSIPHISIHPDPLSYNGPVTLYLSRYDTNKDVLCVHTGFMSEGHHDIKTVFGDCGGMLFDPKGRLLGLHCAGSDDVVFMDTTTGKSNIWTSYKLQHPSEIMITLNNEINLPNPANYDFETTKVVYQHPLRNVCATLETLQHLTNKTNAKLPYDSRLLSDFNITAEQYNQYGYYIDYNNFVNNFNRYTTTTIGTKSFETCIKYGLMD 305
                                    10        20        30        40        50        60        70        80        90       100       110       120    || 132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302   
                                                                                                                                                      125|                                                                                                                                                                                 
                                                                                                                                                       128                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh.eeee...eeee.eee..eeeee.hhhh...hhhhhh.........hhhhheee..eeeee..............hhhh.eeeeeeeeee.....eeeeeeeeee........hhhhh..eeee....eeeeeeeee........................eeeee.........hhhhh..........hhhhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lak D   1 SAASNPSISHIVLEMPVAINPLIKYTTVSSLRGAVVNGYIYIQRHLFGSKEFEACYNCKNLERSKYDIDSAELIGTLIRIPLHDKHSIPHISIHPDPLSYNGPVTLYLSRYDTEDVLCVHTGFMSEGHHDIKTVFGDCGGMLFDPKGRLLGLHCAGSDDVVFMDTTTGKSNIWTSYKLQHPSEIMITLNNEINLPNPANYDKVVYQHPLRNVCATLETLQHLTNKTNAKLPYDSRLLSDFNITAEQYNQYGYYIDYNNFVNNFNRYTTTTIGTKSFETCIKYGLMD 305
                                    10        20      ||33        43        53|     ||72        82        92       102       112       122   ||  135       145       155       165       175       185       195       205       215||     229       239       249       259       269       279       289       299      
                                                     27|                    53|    62|                                                     126|                                                                                   216|                                                                                    
                                                      31                     56     70                                                      130                                                                                    221                                                                                    


Chain I from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5lak I   1 xYYNx   5
                            |   |
                            1-BEZ
                                5-ECC


Chain J from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5lak J   1 xYYNx   5
                            |   |
                            |   |
                            1-BEZ
                                5-ECC


Chain K from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5lak K   1 xYYNx   5
                            |   |
                            |   |
                            1-BEZ
                                5-ECC
   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  (0, 0)

(no "SCOP Domain" information available for 5LAK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LAK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LAK)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5LAK)

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 Related Entries

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        F8RL29_AMV79 | F8RL29: 5lac

(-) Related Entries Specified in the PDB File

5lac 5LAC IS THE SEMET-LABELED DERIVATIVE FOR STRUCTURE SOLUTION.