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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS3 HELICASE INHIBITOR CO-COMPLEX WITH COMPOUND 7 [[1-(3-CHLOROBENZYL)-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 :  2.30
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
12SY1Ligand/Ion[1-(3-CHLOROBENZYL)-1H-INDOL-3-YL]ACETIC ACID
2CA2Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL 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 , TYR A:502BINDING SITE FOR RESIDUE 2SY A 701
2AC2SOFTWAREASP A:437 , HOH A:839 , ASP B:437 , HOH B:704 , HOH B:737 , HOH B:750BINDING SITE FOR RESIDUE CA A 702
3AC3SOFTWAREASP A:437 , GLU A:447 , HOH A:839 , ASP B:437BINDING SITE FOR RESIDUE CA A 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OK3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:360 -Gly A:361
2Ser A:398 -Val A:399
3Asp A:441 -Pro A:442
4Asp B:441 -Pro B:442

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OK3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OK3)

(-) Exons   (0, 0)

(no "Exon" information available for 4OK3)

(-) 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:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4ok3a1 A:187-325 HCV helicase domain                                                                                                      d4ok3a2 A:326-629 HCV helicase domain                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeee.hhhhh..hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh...eee....ee.....eeeeehhhhhhh.........eeee......hhhhhhhhhhhhhhhhhhh..eeeeee.............eeeee..............hhhhh...eeeee..hhhhhh.......ee......eeeee...........eeee..eeeeeeee.......eeeeeeee.hhhhhhhhhh.......eeeee...........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........ee..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ok3 A 187 NSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATPPGSVTVSHPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLNAVASVIPDVVVVSTDALMTGGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFVAPGERPSGMFDSSVLCECYDAGCAWYELMPAETTVRLRAYMNTPGLPVCQDHLEFWEGVFTGLTHIDAHFLSQTKQSGENFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMTCMSADLEV 629
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376    || 398  ||   411     ||423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623      
                                                                                                                                                                                                                            381|  ||  ||         417|                                                                                                                                                                                                                 
                                                                                                                                                                                                                             387  ||  ||          420                                                                                                                                                                                                                 
                                                                                                                                                                                                                                390|  ||                                                                                                                                                                                                                              
                                                                                                                                                                                                                                 398  ||                                                                                                                                                                                                                              
                                                                                                                                                                                                                                    401|                                                                                                                                                                                                                              
                                                                                                                                                                                                                                     405                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4ok3b1 B:187-325 HCV helicase domain                                                                                     d4ok3b2 B:326-628 HCV helicase domain                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeee........hhhhhhhhhh...eeeee..................eeeeehhhhhhh.........eeee......hhhhhhhhhhhhhhh......eeeeee.............eeeee......eee..eeehhhhh...eeeee..hhhhhhhhhhhhhh....eeee..............eeeee........eeee..eeeeeeee.......eeeeeeee.hhhhhhhhhhh......eeeee...........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhh.........ee...........ee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ok3 B 187 NSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKASPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATPPGSVTVSHPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTNGDVVVVSTDALGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFVAPGERPSGMFDSSVLCECYDAGCAWYELMPAETTVRLRAYMNTPGLPVCQDHLEFWEGVFTGLTHIDAHFLSQTKQSGENFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMTCMSADLE 628
                                   196       206       216       226       236       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413||     428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628
                                                                                    245|                                                                                                                                                    414|                                                                                                                                                                                                                
                                                                                     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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OK3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OK3)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ser A:398 - Val A:399   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        K4KA16_9HEPC | K4KA16: 4cl1 4ojq 4ok5 4ok6 4oks

(-) Related Entries Specified in the PDB File

4ojq 4ok5 4ok6 4oks