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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS3 HELICASE INHIBITOR CO-COMPLEX WITH COMPOUND 9 [1-(3-ETHYNYLBENZYL)-1H-INDOL-3-YL]ACETIC ACID]
 
Authors :  A. K. Padyana
Date :  21 Jan 14  (Deposition) - 05 Mar 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hepatitis, Atpase, Ntpase, Ns3 Helicase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Laplante, A. K. Padyana, A. Abeywardane, P. Bonneau, M. Cartier, R. Coulombe, A. Jakalian, J. Wildeson-Jones, X. Li, S. Liang, G. Mckercher, P. White, Q. Zhang, S. J. Taylor
Integrated Strategies For Identifying Leads That Target The Ns3 Helicase Of The Hepatitis C Virus.
J. Med. Chem. V. 57 2074 2014
PubMed-ID: 24467709  |  Reference-DOI: 10.1021/JM401432C

(-) Compounds

Molecule 1 - SERINE PROTEASE NS3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1206-1656
    Gene: NS3
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
12T21Ligand/Ion[1-(3-ETHYNYLBENZYL)-1H-INDOL-3-YL]ACETIC ACID
2CA2Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:437 , HOH A:1138 , HOH A:1139 , HOH A:1147 , ASP B:437 , HOH B:701 , HOH B:781BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWAREASP A:437 , GLU A:447 , HOH A:1139 , ASP B:437BINDING SITE FOR RESIDUE CA A 1002
3AC3SOFTWAREVAL A:232 , GLY A:255 , THR A:269 , GLY A:271 , LYS A:272 , ALA A:275 , ALA A:297 , THR A:298 , ALA A:497 , TYR A:502BINDING SITE FOR RESIDUE 2T2 A 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OK5)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:360 -Gly A:361
2Asp A:441 -Pro A:442
3Asp B:441 -Pro B:442

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OK5)

(-) Exons   (0, 0)

(no "Exon" information available for 4OK5)

(-) 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:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4ok5a1 A:184-325 HCV helicase domain                                                                                                         d4ok5a2 A:326-629 HCV helicase domain                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..........eeeeee........hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh...eee....ee.....eeeeehhhhhhh.........eeeee.....hhhhhhhhhhhhhhh......eeeeee.............eeeee......eee..eeehhhhhh..eeeee....hhhhhhhhh.......ee.............eeeee...........eeee..eeeeeeee.......eeeeeeee.hhhhhhhhhhh......eeeee...........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhh.........ee...........ee..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ok5 A 184 FTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATPPGSVTVSHPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPDVVVVSTDALMTTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFVAPGERPSGMFDSSVLCECYDAGCAWYELMPAETTVRLRAYMNTPGLPVCQDHLEFWEGVFTGLTHIDAHFLSQTKQSGENFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMTCMSADLEV 629
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       406       416|      428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628 
                                                                                                                                                                                                                                                   401|        416|                                                                                                                                                                                                                  
                                                                                                                                                                                                                                                    405         419                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4ok5b1 B:187-325 HCV helicase domain                                                                                  d4ok5b2 B:326-629 HCV helicase domain                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeee....hhhhhhhhh...eeeee....................eeeeehhhhhhh.........eeee......hhhhhhhhhhhhhhh......eeeeee.............eeeee......eee..eeehhhhh...eeeee..hhhhhhhhhhhhhh....eeee..............eeeee..........eeee..eeeeeeee.......eeeeeeee.hhhhhhhhhh.......eeeee...........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........ee..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ok5 B 187 NSSPPAVPQSFQVAHLHAPTTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATPPGSVTVSHPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTNGDVVVVSTDALMTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFVAPGERPSGMFDSSVLCECYDAGCAWYELMPAETTVRLRAYMNTPGLPVCQDHLEFWEGVFTGLTHIDAHFLSQTKQSGENFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMTCMSADLEV 629
                                   196       206|      221       231       241     ||266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629
                                             206|                                247|                                                                                                                                                     415|                                                                                                                                                                                                                  
                                              212                                 263                                                                                                                                                      419
   Legend:   → Mismatch (orange background)
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  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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OK5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OK5)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ok5
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 Related Entries

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

UniProtKB/TrEMBL
        K4KA16_9HEPC | K4KA16: 4cl1 4ojq 4ok3 4ok6 4oks

(-) Related Entries Specified in the PDB File

4ojq 4ok3 4ok6 4oks