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(-) Description

Title :  CRYSTAL STRUCTURE OF HCV NS3/NS4A PROTEASE COMPLEXED WITH COMPOUND 4
 
Authors :  C. T. Lemke
Date :  23 Nov 12  (Deposition) - 02 Jan 13  (Release) - 13 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Hepatitis C Virus, Ns3, Ns4A, Protein-Inhibitor Complex Compound 4, Serine Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. O'Meara, C. T. Lemke, C. Godbout, G. Kukolj, L. Lagace, B. Moreau, D. Thibeault, P. W. White, M. Llinas-Brunet
Molecular Mechanism By Which A Potent Hepatitis C Virus Ns3-Ns4A Protease Inhibitor Overcomes Emergence Of Resistance.
J. Biol. Chem. V. 288 5673 2013
PubMed-ID: 23271737  |  Reference-DOI: 10.1074/JBC.M112.439455

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    Chains: A, B
    EC Number: 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: NS3 PROTEASE DOMAIN (UNP RESIDUES 1027-1206)
    Gene: POLG_HCVJA
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11116
    Strain: ISOLATE JAPANESE
    Synonym: CORE PROTEIN P21, CAPSID PROTEIN C, P21, CORE PROTEIN P19, ENVELOPE GLYCOPROTEIN E1, GP32, GP35, ENVELOPE GLYCOPROTEIN E2, NS1, GP68, GP70, P7, PROTEASE NS2-3, P23, SERINE PROTEASE NS3, HEPACIVIRIN, NS3P, P70, NON-STRUCTURAL PROTEIN 4A, NS4A, P8, NON- STRUCTURAL PROTEIN 4B, NS4B, P27, NON-STRUCTURAL PROTEIN 5A, NS5A, P56, RNA-DIRECTED RNA POLYMERASE, NS5B, P68
 
Molecule 2 - HCV NON-STRUCTURAL PROTEIN 4A
    Chains: C, D
    Engineered: YES
    Fragment: NS3 INTERACTING PEPTIDE (UNP RESIDUES 1678-1691)
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11116
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
11BV2Ligand/Ion(2R,6S,7E,10E,13AR,14AR,16AS)-2-{[7-METHOXY-8-METHYL-2-(PROPAN-2-YLOXY)QUINOLIN-4-YL]OXY}-N-[(1-METHYLCYCLOPROPYL)SULFONYL]-6-{[(1-METHYL-1H-PYRAZOL-3-YL)CARBONYL]AMINO}-5,16-DIOXO-1,2,3,6,9,12,13,13A,14,15,16,16A-DODECAHYDROCYCLOPROPA[E]PYRROLO[1,2-A][1,4]DIAZACYCLOPENTADECINE-14A(5H)-CARBOXAMIDE
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11BV1Ligand/Ion(2R,6S,7E,10E,13AR,14AR,16AS)-2-{[7-METHOXY-8-METHYL-2-(PROPAN-2-YLOXY)QUINOLIN-4-YL]OXY}-N-[(1-METHYLCYCLOPROPYL)SULFONYL]-6-{[(1-METHYL-1H-PYRAZOL-3-YL)CARBONYL]AMINO}-5,16-DIOXO-1,2,3,6,9,12,13,13A,14,15,16,16A-DODECAHYDROCYCLOPROPA[E]PYRROLO[1,2-A][1,4]DIAZACYCLOPENTADECINE-14A(5H)-CARBOXAMIDE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11BV1Ligand/Ion(2R,6S,7E,10E,13AR,14AR,16AS)-2-{[7-METHOXY-8-METHYL-2-(PROPAN-2-YLOXY)QUINOLIN-4-YL]OXY}-N-[(1-METHYLCYCLOPROPYL)SULFONYL]-6-{[(1-METHYL-1H-PYRAZOL-3-YL)CARBONYL]AMINO}-5,16-DIOXO-1,2,3,6,9,12,13,13A,14,15,16,16A-DODECAHYDROCYCLOPROPA[E]PYRROLO[1,2-A][1,4]DIAZACYCLOPENTADECINE-14A(5H)-CARBOXAMIDE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:5 , ALA A:111 , HOH A:306 , HOH A:325 , HOH A:327 , HOH A:340BINDING SITE FOR RESIDUE NA A 201
2AC2SOFTWAREGLN A:41 , SER A:42 , PHE A:43 , TYR A:56 , HIS A:57 , GLY A:58 , VAL A:78 , ASP A:79 , ASP A:81 , ARG A:123 , VAL A:132 , LEU A:135 , LYS A:136 , GLY A:137 , SER A:138 , SER A:139 , PHE A:154 , ARG A:155 , ALA A:156 , ALA A:157 , HOH A:342 , HOH A:348BINDING SITE FOR RESIDUE 1BV A 202
3AC3SOFTWAREALA B:5 , ALA B:111 , HOH B:308 , HOH B:320 , HOH B:328 , HOH B:331BINDING SITE FOR RESIDUE NA B 201
4AC4SOFTWAREGLN B:41 , SER B:42 , PHE B:43 , TYR B:56 , HIS B:57 , GLY B:58 , VAL B:78 , ASP B:79 , ASP B:81 , ARG B:123 , VAL B:132 , LEU B:135 , LYS B:136 , GLY B:137 , SER B:138 , SER B:139 , PHE B:154 , ARG B:155 , ALA B:156 , ALA B:157 , ASP B:168 , HOH B:326 , HOH B:349BINDING SITE FOR RESIDUE 1BV B 202

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:47 -A:52
2A:97 -A:145
3B:47 -B:52

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:1 -Pro A:2
2Ala B:1 -Pro B:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I31)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I31)

(-) Exons   (0, 0)

(no "Exon" information available for 4I31)

(-) 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
                 4i31 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..eeeeeeeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i31 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
                 4i31 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
                 4i31 D 220 KGSVVIVGRIILS 232
                                   229
   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 4I31)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I31)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I31)

(-) Gene Ontology  (74, 74)

Asymmetric Unit(hide GO term definitions)

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

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