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(-) Description

Title :  HCV NS3 PROTEASE WITH NS4A PEPTIDE AND A COVALENTLY BOUND MACROCYCLIC KETOAMIDE COMPOUND.
 
Authors :  K. X. Chen, F. G. Njoroge, A. Prongay, J. Pichardo, V. Madison, V. Girijavallabhan
Date :  29 Jun 05  (Deposition) - 04 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. X. Chen, F. G. Njoroge, A. Prongay, J. Pichardo, V. Madison, V. Girijavallabhan
Synthesis And Biological Activity Of Macrocyclic Inhibitors Of Hepatitis C Virus (Hcv) Ns3 Protease
Bioorg. Med. Chem. Lett. V. 15 4475 2005
PubMed-ID: 16112859  |  Reference-DOI: 10.1016/J.BMCL.2005.07.033
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NS3 PROTEASE/HELICASE'
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PROTEASE DOMAIN, RESIDUES 1-181
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
 
Molecule 2 - NS4A PEPTIDE
    Chains: B, D
    Engineered: YES
    Fragment: RESIDUES 21-39
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HEPATITIS C VIRUS TYPE 1B.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2FNH1Ligand/Ion(2R)-({N-[(3S)-3-({[(3S,6S)-6-CYCLOHEXYL-5,8-DIOXO-4,7-DIAZABICYCLO[14.3.1]ICOSA-1(20),16,18-TRIEN-3-YL]CARBONYL}AMINO)-2-OXOHEXANOYL]GLYCYL}AMINO)(PHENYL)ACETIC ACID
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:97 , CYS A:99 , CYS A:145 , HOH A:433BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWARECYS C:97 , CYS C:99 , CYS C:145 , HOH C:303BINDING SITE FOR RESIDUE ZN C 302
3AC3SOFTWARELEU A:13 , CYS A:16 , ILE A:17 , THR A:38BINDING SITE FOR RESIDUE BME A 201
4AC4SOFTWAREGLN A:41 , THR A:42 , HIS A:57 , LEU A:135 , LYS A:136 , GLY A:137 , SER A:138 , SER A:139 , ARG A:155 , ALA A:156 , ALA A:157 , CYS A:159 , ASP A:168BINDING SITE FOR RESIDUE FNH A 401

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1C:97 -C:145

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A4Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A4Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A4Q)

(-) Exons   (0, 0)

(no "Exon" information available for 2A4Q)

(-) Sequences/Alignments

Asymmetric/Biological 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:181
 aligned with Q91RS4_9HEPC | Q91RS4 from UniProtKB/TrEMBL  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
         Q91RS4_9HEPC     1 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRS 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2a4qA01 A:1-94  [code=2.40.10.120, no name defined]                                           2a4qA02 A:95-181 Trypsin-like serine proteases                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeeehhhhh..............eee....eeeee................eeeee.....eeeeee....eeeeeeeeehhhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a4q A   1 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRS 181
                                    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:22
 aligned with O39914_9HEPC | O39914 from UniProtKB/TrEMBL  Length:88

    Alignment length:22
                                    14        24  
         O39914_9HEPC     5 TGSVVIVGRIILSGKPAIIPDR  26
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 2a4q B  20 KGSVVIVGRIVLSGKPAIIPKK  41
                                    29        39  


Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q91RS4_9HEPC | Q91RS4 from UniProtKB/TrEMBL  Length:181

    Alignment length:151
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178 
         Q91RS4_9HEPC    29 VEGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTM 179
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2a4qC01 C:29-94  [code=2.40.10.120, no name defined]              2a4qC02 C:95-179 Trypsin-like serine proteases                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeeeeee..eeeeehhhhh..ee..........eeehhh.eeeee................eeeee.....eeeeeeee..eeeeeeeee.hhh......eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a4q C  29 VEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTM 179
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178 


Chain D from PDB  Type:PROTEIN  Length:16
 aligned with O39914_9HEPC | O39914 from UniProtKB/TrEMBL  Length:88

    Alignment length:16
                                    15      
         O39914_9HEPC     6 GSVVIVGRIILSGKPA  21
               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
                 2a4q D  21 GSVVIVGRIVLSGKPA  36
                                    30
   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 2A4Q)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A4Q)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (Q91RS4_9HEPC | Q91RS4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0097264    self proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their own peptide bonds.
    GO:0019087    transformation of host cell by virus    Any virus-induced change in the morphological, biochemical, or growth parameters of a cell.

Chain B,D   (O39914_9HEPC | O39914)
biological process
    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.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  2a4q
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  Q91RS4_9HEPC | Q91RS4
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 Related Entries

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

UniProtKB/Swiss-Prot
        O39914_9HEPC | O39914: 2a4r
        Q91RS4_9HEPC | Q91RS4: 1rtl 2a4r
UniProtKB/TrEMBL
        O39914_9HEPC | O39914: 1a1r 1n1l 1rgq 1rtl
        Q91RS4_9HEPC | Q91RS4: 2f9u 2obo 2p59 2xcn

(-) Related Entries Specified in the PDB File

1a1r HCV NS3 PROTEASE DOMAIN: NS4A PEPTIDE COMPLEX
1jxp BK STRAIN HEPATITIS C VIRUS (HCV) NS3-NS4A
1n1l CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN: NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND INHIBITOR (GW472467X)
1ns3 STRUCTURE OF HCV PROTEASE (BK STRAIN)
1rtl CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN: NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND PYRROLIDINE-5,5-TRANSLACTAM INHIBITOR
2a4g HCV PROTEASE NS3 WITH NS4A PEPTIDE AND A COVALENTLY BOUND KETOAMIDE.