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(-) Description

Title :  CRYSTAL STRUCTURE OF HCV NS3 PROTEASE WITH A BORONATE INHIBITOR
 
Authors :  X. Li, Y. -K. Zhang, Y. Liu, C. Z. Ding, Q. Li, Y. Zhou, J. J. Plattner, S. J. X. Qian, D. Fan, L. Liao, Z. -J. Ni, G. V. White, J. E. Mordaunt, L. X. Laza M. J. Slater, R. L. Jarvest, P. Thommes, M. Ellis, C. M. Edge, J. A. Hubba P. Nassau, B. Mcdowell, T. J. Skarzynski, P. Rowland, D. O. Somers, W. M. Kazmierski, R. M. Grimes, L. L. Wright, G. K. Smith, W. Zou, J. Wrig L. E. Pennicott
Date :  23 Apr 10  (Deposition) - 02 Jun 10  (Release) - 16 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Li, Y. -K. Zhang, Y. Liu, C. Z. Ding, Q. Li, Y. Zhou, J. J. Plattner, S. J. Baker, X. Qian, D. Fan, L. Liao, Z. -J. Ni, G. V. White, J. E. Mordaunt, L. X. Lazarides, M. J. Slater, R. L. Jarvest, C. M. Edge, J. A. Hubbard, P. Nassau, B. Mcdowell, T. J. Skarzynski, P. Thommes, M. Ellis, P. Rowland, D. O. Somers, W. M. Kazmierski, R. M. Grimes, L. L. Wright, G. K. Smith, W. Zou, J. Wright, L. E. Pennicott
Synthesis And Evaluation Of Novel Alpha-Amino Cyclic Boronates As Inhibitors Of Hcv Ns3 Protease.
Bioorg. Med. Chem. Lett. V. 20 3550 2010
PubMed-ID: 20493689  |  Reference-DOI: 10.1016/J.BMCL.2010.04.129

(-) Compounds

Molecule 1 - NS3 PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PROTEASE DOMAIN, RESIDUES 1-180
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Other Details: TETRAHEDRAL BORATE DERIVATIVE LINKED TO OXYGEN OF S139.
    Strain: H
 
Molecule 2 - NS4A
    Chains: C, D
    Fragment: RESIDUES 21-39
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Other Details: K19, K20, K40 AND K41 ADDED TO FRAGMENT
    Strain: H
    Synonym: NON-STRUCTURAL PROTEIN 4A/B
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1C8D2Ligand/IonN-[(CYCLOPENTYLOXY)CARBONYL]-3-METHYL-L-VALYL-(4R)-N-{(1R)-3-HYDROXY-1-[HYDROXY(OXIDO)BORANYL]PROPYL}-4-(ISOQUINOLIN-1-YLOXY)-L-PROLINAMIDE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:57 , ARG A:123 , LEU A:135 , GLY A:137 , SER A:139 , PHE A:154 , ARG A:155 , ALA A:156 , ALA A:157 , ASP A:168BINDING SITE FOR RESIDUE C8D A1181
2AC2SOFTWAREHIS B:57 , ASP B:81 , ARG B:123 , SER B:139 , ARG B:155 , ALA B:156 , ALA B:157 , ARG B:161 , ASP B:168 , HOH B:2020BINDING SITE FOR RESIDUE C8D B1181
3AC3SOFTWARETHR A:4 , LEU C:31 , GLY C:33 , HOH C:2002BINDING SITE FOR RESIDUE MG C1041
4AC4SOFTWAREALA A:5 , ALA A:111 , HOH A:2014 , HOH B:2013BINDING SITE FOR RESIDUE MG A1182
5AC5SOFTWARECYS A:97 , THR A:98 , CYS A:99 , CYS A:145 , HOH A:2024BINDING SITE FOR RESIDUE ZN A1183
6AC6SOFTWARECYS B:97 , THR B:98 , CYS B:99 , CYS B:145 , HOH B:2021BINDING SITE FOR RESIDUE ZN B1182

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XCN)

(-) 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 2XCN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XCN)

(-) 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:180
 aligned with Q91RS4_9HEPC | Q91RS4 from UniProtKB/TrEMBL  Length:181

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
         Q91RS4_9HEPC     1 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMR 180
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2xcnA01 A:1-94  [code=2.40.10.120, no name defined]                                           2xcnA02 A:95-180 Trypsin-like serine proteases                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeeehhhhh..............eee....eeeee................eeeee.....eeeeee....eeeeeeeee.hhh......eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xcn A   1 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMR 180
                                    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:153
 aligned with Q91RS4_9HEPC | Q91RS4 from UniProtKB/TrEMBL  Length:181

    Alignment length:153
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177   
         Q91RS4_9HEPC    28 QVEGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMR 180
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2xcnB01 B:29-94  [code=2.40.10.120, no name defined]              2xcnB02 B:95-180 Trypsin-like serine proteases                                         CATH domains
           Pfam domains (1) --Peptidase_S29-2xcnB01 B:30-178                                                                                                                       -- Pfam domains (1)
           Pfam domains (2) --Peptidase_S29-2xcnB02 B:30-178                                                                                                                       -- Pfam domains (2)
         Sec.struct. author .....eeeee....eeeeeee..eeeeehhhhh..ee..........eeehhh.eeeee................eeeee.....eeeeee....eeeeeeeee.hhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xcn B  28 QVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMR 180
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177   


Chain C from PDB  Type:PROTEIN  Length:21
 aligned with C9WU77_9HEPC | C9WU77 from UniProtKB/TrEMBL  Length:54

    Alignment length:21
                                    29        39 
         C9WU77_9HEPC    20 AGSVVIVGRIVLSGKPAIIPD  40
               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
                 2xcn C  20 KGSVVIVGRIVLSGKPAIIPK  40
                                    29        39 


Chain D from PDB  Type:PROTEIN  Length:16
 aligned with C9WU77_9HEPC | C9WU77 from UniProtKB/TrEMBL  Length:54

    Alignment length:16
                                    30      
         C9WU77_9HEPC    21 GSVVIVGRIVLSGKPA  36
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
           Pfam domains (1) HCV_NS4a-2xcnD01 Pfam domains (1)
           Pfam domains (2) HCV_NS4a-2xcnD02 Pfam domains (2)
         Sec.struct. author .eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2xcn 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 2XCN)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)
(-)
Clan: no clan defined [family: HCV_NS4a] (14)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 C,D   (C9WU77_9HEPC | C9WU77)
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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  Q91RS4_9HEPC | Q91RS4
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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
        C9WU77_9HEPC | C9WU77: 2xcf 2xni
        Q91RS4_9HEPC | Q91RS4: 2a4q 2f9u 2obo 2p59

(-) Related Entries Specified in the PDB File

2a4q HCV NS3 PROTEASE WITH NS4A PEPTIDE AND A COVALENTLY BOUNDMACROCYCLIC KETOAMIDE COMPOUND.
2a4r HCV NS3 PROTEASE DOMAIN WITH A KETOAMIDE INHIBITORCOVALENTLY BOUND.
2f9u HCV NS3 PROTEASE DOMAIN WITH NS4A PEPTIDE AND A KETOAMIDEINHIBITOR WITH A P2 NORBORANE
2xcf CRYSTAL STRUCTURE OF HCV NS3 PROTEASE WITH A BORONATE INHIBITOR