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(-) Description

Title :  HCV NS3 PROTEASE DOMAIN WITH NS4A PEPTIDE AND A KETOAMIDE INHIBITOR WITH A P2 NORBORANE
 
Authors :  S. Venkatraman, F. G. Njoroge, W. Wu, V. Girijavallabhan, A. J. Prongay, N. Butkiewicz, J. Pichardo
Date :  06 Dec 05  (Deposition) - 06 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hcv, Hepatitis C Protease, Ns3 Protease, Ketoamide Inhibitor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Venkatraman, F. G. Njoroge, W. Wu, V. Girijavallabhan, A. J. Prongay, N. Butkiewicz, J. Pichardo
Novel Inhibitors Of Hepatitis C Ns3-Ns4A Serine Protease Derived From 2-Aza-Bicyclo[2. 2. 1]Heptane-3-Carboxylic Acid.
Bioorg. Med. Chem. Lett. V. 16 1628 2006
PubMed-ID: 16413182  |  Reference-DOI: 10.1016/J.BMCL.2005.12.046
(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 Plasmid: NS3(181)HIS6/PET22B
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NS3 PROTEASE DOMAIN ( RESIDUES 1027-1207 OF THE POLYPROTEIN).
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Strain: H STRAIN
 
Molecule 2 - POLYPROTEIN
    Chains: B, D
    Engineered: YES
    Other Details: SOLID-PHASE PEPTIDE SYNTHESIS OF THE NS4A RESIDUES 21-39 PEPTIDE WITH N-TERMINAL KK AND C-TERMINAL KK EXTENSIONS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
15NH1Ligand/Ion1,1-DIMETHYLETHYL [1-CYCLOHEXYL-2-[3-[[[1-[2-[[2-[[2-(DIMETHYLAMINO)-2-OXO-1-PHENYLETHYL]AMINO]-2-OXOETHYL]AMINO]-1,2-DIOXOETHYL]PENTYL]AMINO]CARBONYL]-2-AZABICYCLO[2.2.1]HEPTAN-2-YL]-2-OXOETHYL]CARBAMATE
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:97 , CYS A:99 , CYS A:145 , HOH A:1013BINDING SITE FOR RESIDUE ZN A 901
2AC2SOFTWARECYS C:97 , CYS C:99 , CYS C:145 , HOH C:902BINDING SITE FOR RESIDUE ZN C 901
3AC3SOFTWARETHR A:40 , GLN A:41 , THR A:42 , HIS A:57 , ILE A:132 , 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:168 , HOH A:1009BINDING SITE FOR RESIDUE 5NH A 999

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:97 -A:99

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F9U)

(-) Exons   (0, 0)

(no "Exon" information available for 2F9U)

(-) 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:183
 aligned with Q91RS4_9HEPC | Q91RS4 from UniProtKB/TrEMBL  Length:181

    Alignment length:183
                                                                                                                                                                                                              181  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|  
         Q91RS4_9HEPC     1 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRS--   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2f9uA01 A:1-94  [code=2.40.10.120, no name defined]                                           2f9uA02 A:95-183 Trypsin-like serine proteases                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeeehhhhh...eee..eee...eee....eeeee................eeeee.....eeeeee....eeeeeeeeehhhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f9u A   1 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRSGS 183
                                    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:23
                                                       
               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
                 2f9u B  19 KKGSVVIVGRIVLSGKPAIIPKK  41
                                    28        38   


Chain C from PDB  Type:PROTEIN  Length:152
 aligned with Q91RS4_9HEPC | Q91RS4 from UniProtKB/TrEMBL  Length:181

    Alignment length:152
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  
         Q91RS4_9HEPC    28 QVEGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTM 179
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2f9uC01 C:29-94  [code=2.40.10.120, no name defined]              2f9uC02 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.hhhh.....eee.....eeeeeeeeee...eeeeeeeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f9u C  28 QVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTM 179
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  


Chain D from PDB  Type:PROTEIN  Length:19
                                                   
               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
                 2f9u D  21 GSVVIVGRIVLSGKPAIIP  39
                                    30
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2F9U)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F9U)

(-) Gene Ontology  (6, 6)

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q91RS4_9HEPC | Q91RS4: 1rtl 2a4r
UniProtKB/TrEMBL
        Q91RS4_9HEPC | Q91RS4: 2a4q 2obo 2p59 2xcn

(-) Related Entries Specified in the PDB File

1a1r SAME PROTEIN WITHOUT INHIBITOR
1jxp A DIFFERENT STRAIN OF THE SAME PROTEIN
1n1l SAME PROTEIN WITH A DIFFERENT INHIBITOR
2a4g SAME PROTEIN WITH A DIFFERENT INHIBITOR
2a4q SAME PROTEIN WITH A DIFFERENT INHIBITOR
2a4r SAME PROTEIN WITH A DIFFERENT INHIBITOR