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(-) Description

Title :  CRYSTAL STRUCTURE OF HCV NS3/NS4A PROTEASE COMPLEXED WITH DDIVPC PEPTIDE
 
Authors :  C. T. Lemke
Date :  14 Mar 13  (Deposition) - 30 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Hepatitis C Virus, Serine Protease, Ddivpc, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Laplante, C. T. Lemke
Importance Of The Peptide Scaffold Of Drugs That Target The Hepatitis C Virus Ns3 Protease And Its Crucial Bioactive Conformation And Dynamic Factors.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POLYPROTEIN
    Chains: A, B
    EC Number: 3.4.21.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: NS3 PROTEASE DOMAIN
    Gene: POLG_HCVJA
    Organism Scientific: HEPATITIS C VIRUS GENOTYPE 2
    Organism Taxid: 40271
 
Molecule 2 - HCV NON-STRUCTURAL PROTEIN 4A
    Chains: C, D
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES
 
Molecule 3 - SUBSTRATE PEPTIDE
    Chains: E, F
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C E 
Biological Unit 2 (1x):  B D F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:97 , CYS A:99 , CYS A:145 , HOH A:301BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREALA A:5 , ALA A:111 , HOH A:308 , HOH A:336 , HOH A:340 , HOH A:342BINDING SITE FOR RESIDUE NA A 202
3AC3SOFTWARECYS B:97 , CYS B:99 , CYS B:145 , HOH B:301BINDING SITE FOR RESIDUE ZN B 201
4AC4SOFTWAREALA B:5 , ALA B:111 , HOH B:308 , HOH B:361 , HOH B:379BINDING SITE FOR RESIDUE NA B 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JMY)

(-) 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:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeeehhhhh..............eee....eeeee................eeeee.....eeeeee....eeeeeeeeehhhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jmy A   1 APITAYSQQTRGLLGCIITSLTGRDKNQVDGEVQVLSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWPAPPGARSMTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHVVGIFRAAVCTRGVAKAVDFIPVESMETTMRAS 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  


Chain B from PDB  Type:PROTEIN  Length:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeeehhhhh..............eee....eeeee................eeeee.....eeeeee....eeeeeeeeehhhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jmy B   1 APITAYSQQTRGLLGCIITSLTGRDKNQVDGEVQVLSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWPAPPGARSMTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHVVGIFRAAVCTRGVAKAVDFIPVESMETTMRAS 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  


Chain C from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4jmy C 220 KGSVVIVGRIILS 232
                                   229   


Chain D from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4jmy D 220 KGSVVIVGRIILS 232
                                   229   


Chain E from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author .eeee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4jmy E   1 DDIVPC   6


Chain F from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author .eeee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4jmy F   1 DDIVPC   6
   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 4JMY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 103)

Asymmetric Unit(hide GO term definitions)

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  4jmy
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  POLG_HCVJA | P26662
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  Q81817_9HEPC | Q81817
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_HCVJA | P26662: 1dxp 1dy8 1dy9 1w3c 2k8j 3oyp 3p8n 3p8o 4a1t 4a1v 4a1x 4i31 4i32 4i33 4ktc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JMY)