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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS3 HELICASE INHIBITOR CO-COMPLEX WITH COMPOUND 13 [[1-(2-METHOXY-5-NITROBENZYL)-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 :  2.40
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
12T71Ligand/Ion[1-(2-METHOXY-5-NITROBENZYL)-1H-INDOL-3-YL]ACETIC ACID
2CA2Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:437 , HOH A:1133 , ASP B:437 , HOH B:791BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWAREASP A:437 , GLU A:447 , HOH A:1142 , ASP B:437 , HOH B:718BINDING SITE FOR RESIDUE CA A 1002
3AC3SOFTWAREVAL A:232 , THR A:254 , GLY A:255 , THR A:269 , GLY A:271 , LYS A:272 , ALA A:275 , THR A:298 , ALA A:497 , TRP A:501 , TYR A:502BINDING SITE FOR RESIDUE 2T7 A 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OK6)

(-) 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 4OK6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OK6)

(-) Exons   (0, 0)

(no "Exon" information available for 4OK6)

(-) 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:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4ok6a1 A:185-325 HCV helicase domain                                                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..........eeeeee........hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh...eee....ee.....eeeeehhhhhhh.........eeeee.....hhhhhhhhhhhhhhh......eeeeee.............eee................hhhhhh..eeeee..hhhhhhhhhhhh...eee.........eeeee.......eeee..eeeeeeee.......eeeeeeee.hhhhhhhhhhh......eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhh.........ee...........ee..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ok6 A 185 TDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATPPGSVTVSHPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLINAVAYYRGLDVSVDVVVVSTDALMFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFVAPGERPSGMFDSSVLCECYDAGCAWYELMPAETTVRLRAYMNTPGLPVCQDHLEFWEGVFTGLTHIDAHFLSQTKQSGENFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMTCMSADLEV 629
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374      |388       398||     413 ||    429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629
                                                                                                                                                                                                                              381|          399|       415|                                                                                                                                                                                                               
                                                                                                                                                                                                                               386           405        422                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4ok6b1 B:187-325 HCV helicase domain                                                                                 d4ok6b2 B:326-627 HCV helicase domain                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee....hhhhhhhh....eeeee...................eeeeehhhhhhh.........eeee......hhhhhhhhhhhhhhh......eeeeee.............eeeee......eee..eeehhhhh...eeeee..hhhhhhhhhhhhhh....eeee..............eeeee........eeee..eeeeeeee.......eeeeeeee.hhhhhhhhhh.......eeeee...........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhh.........ee...........ee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ok6 B 187 NSSPPAVPQSFQVAHLHAPTTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATPPGSVTVSHPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTNGDVVVVSTDALGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFVAPGERPSGMFDSSVLCECYDAGCAWYELMPAETTVRLRAYMNTPGLPVCQDHLEFWEGVFTGLTHIDAHFLSQTKQSGENFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMTCMSADL 627
                                   196       206|      221       231       241    || 267       277       287       297       307       317       327       337       347       357       367       377       387       397       407      |422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622     
                                             206|                               246|                                                                                                                                                    414|                                                                                                                                                                                                               
                                              212                                263                                                                                                                                                     420
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OK6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OK6)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ok6
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 Related Entries

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

UniProtKB/TrEMBL
        K4KA16_9HEPC | K4KA16: 4cl1 4ojq 4ok3 4ok5 4oks

(-) Related Entries Specified in the PDB File

4ojq 4ok3 4ok5 4oks