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(-) Description

Title :  STRUCTURE OF HEPATITIS C VIRUS (HCV) FULL-LENGTH NS3 COMPLEX WITH SMALL-MOLECULE LIGAND 5-BROMO-1-METHYL-1H-INDOLE-2-CARBOXYLIC ACID (AT21457) IN AN ALTERNATE BINDING SITE.
 
Authors :  T. G. Davies, H. Jhoti, R. F. Ludlow, H. K. Saini, I. J. Tickle, M. Verdonk
Date :  03 Dec 15  (Deposition) - 23 Dec 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hepatitis C Virus, Hcv, Ns3 Complex, Protease-Helicase, Hydrolase, Protein-Ligand Complex, Fragment Screening, Alternate Binding Site, At21457. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. F. Ludlow, M. L. Verdonk, H. K. Saini, I. J. Tickle, H. Jhoti
Detection Of Secondary Binding Sites In Proteins Using Fragment Screening.
Proc. Natl. Acad. Sci. Usa V. 112 15910 2015
PubMed-ID: 26655740  |  Reference-DOI: 10.1073/PNAS.1518946112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE PROTEASE NS3
    Chains: A, B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET17
    Expression System Vector Type: PLASMID
    Organism Scientific: HEPATITIS C VIRUS (ISOLATE BK)
    Organism Taxid: 11105
    Strain: GENOTYPE 1B
    Synonym: HEPACIVIRIN, NS3P, P70

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1R2N2Ligand/Ion5-BROMO-1-METHYL-1H-INDOLE-2-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:370 , LYS B:371 , VAL B:432 , HOH B:2200BINDING SITE FOR RESIDUE R2N B1721
2AC2SOFTWARESER A:370 , LYS A:371 , VAL A:432 , GLN A:434 , HOH A:2403BINDING SITE FOR RESIDUE R2N A1721

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FPY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:441 -Pro A:442
2Asp B:441 -Pro B:442

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FPY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FPY)

(-) Exons   (0, 0)

(no "Exon" information available for 5FPY)

(-) 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:645
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.......eeeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeehhhhhh...eee..eee...eee....eeeee................eeeee.....eeeeee....eeeeeeeee.hhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhhhh................eeeeee........hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.....eee....ee.....eeeeehhhhhhh.........eeeee.....hhhhhhhhhhhhhhh......eeeeee.............eeeee......eee..eeehhhhhhh.eeeee..hhhhhhhhhhhhhhh...eeee....hhhhh.....eeeee..hhhhhh.....eeee..eeeeeeee.......eeeeeeee.hhhhhhhhhh.......eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........ee..hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fpy A 705 GSVVIVGRIILSGSGSITAYSQQTRGLLGCIITSLTGRDKNQVEGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRTITTGAPVTYSTYGKFLADGGCSGGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAIRGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGRRGIYRFVTPGERPSGMFDSSVLCECYDAGCAWYELTPAETSVRLRAYLNTPGLPVCQDHLEFWESVFTGLTHIDAHFLSQTKQAGDNFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMACMSADLEVVT 631
                                   714     ||  6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626     
                                         720|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                            3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:642
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee....eeeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeehhhhhh...eee..eee...eee....eeeee................eeeee.....eeeeee....eeeeeeeee.hhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhhhh................eeeeee........hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh....eee....ee.....eeeeehhhhhhh.........eeeee.....hhhhhhhhhhhhhhh......eeeeee.............eeeee......eee..eeehhhhhh..eeeee..hhhhhhhhhhhhhhh...eeee....hhhhh.....eeeee..hhhhhh.....eeee..eeeeeeee.......eeeeeeee.hhhhhhhhhh.......eeeee...........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhh......ee...........ee..hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fpy B 705 GSVVIVGRIILSSITAYSQQTRGLLGCIITSLTGRDKNQVEGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRTITTGAPVTYSTYGKFLADGGCSGGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAIRGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGRRGIYRFVTPGERPSGMFDSSVLCECYDAGCAWYELTPAETSVRLRAYLNTPGLPVCQDHLEFWESVFTGLTHIDAHFLSQTKQAGDNFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMACMSADLEVVT 631
                                   714 |||     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629  
                                     716||                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                      720|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                         3
   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 5FPY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FPY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FPY)

(-) Gene Ontology  (73, 73)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_HCVBK | P26663: 1a1q 1bt7 1c2p 1csj 1cu1 1gx5 1gx6 1jxp 1nhu 1nhv 1ns3 1os5 1quv 2awz 2ax0 2ax1 2brk 2brl 2dxs 2giq 2gir 2hai 2hwh 2hwi 2i1r 2jc0 2jc1 2o5d 2wcx 2who 2wrm 2xwy 2zku 3br9 3bsa 3bsc 3cde 3ciz 3cj0 3cj2 3cj3 3cj4 3cj5 3co9 3cvk 3cwj 3d28 3d5m 3e51 3fqk 3frz 3g86 3gyn 3h2l 3h59 3h5s 3h5u 3h98 3igv 3mf5 3rvb 3ua7 3udl 3vqs 4a92 4b6e 4b6f 4b71 4b73 4b74 4b75 4b76 4dgv 4dgy 4eo6 4eo8 4ih5 4ih6 4ih7 4k8b 4kai 4kb7 4kbi 4ke5 4mia 4mib 4mk7 4mk8 4mk9 4mka 4mkb 4tn2 4wxp 5fps 5fpt 8ohm

(-) Related Entries Specified in the PDB File

5fp5 STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 WITH SMALL- MOLECULE LIGAND 4-FLUOROBENZOIC ACID (AT222) IN AN ALTERNATE BINDING SITE.
5fp6 STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 WITH SMALL- MOLECULE LIGAND 3-(4,7-DICHLORO-1H-INDOL-3-YL)PROP -2-YN-1-OL (AT17833) IN AN ALTERNATE BINDING SITE.
5fpd STRUCTURE OF HEAT SHOCK-RELATED 70KDA PROTEIN 2 WITH SMALL-MOLECULE LIGAND PYRAZINE-2-CARBOXAMIDE (AT513) IN AN ALTERNATE BINDING SITE.
5fpe STRUCTURE OF HEAT SHOCK-RELATED 70KDA PROTEIN 2 WITH SMALL-MOLECULE LIGAND 1H-1,2,4-TRIAZOL-3-AMINE ( AT485) IN AN ALTERNATE BINDING SITE.
5fpm STRUCTURE OF HEAT SHOCK-RELATED 70KDA PROTEIN 2 WITH SMALL-MOLECULE LIGAND 5-PHENYL-1,3,4-OXADIAZOLE-2- THIOL (AT809) IN AN ALTERNATE BINDING SITE.
5fpn STRUCTURE OF HEAT SHOCK-RELATED 70KDA PROTEIN 2 WITH SMALL-MOLECULE LIGAND 3,5-DIMETHYL-1H-PYRAZOLE-4- CARBOXYLIC ACID (AT9084) IN AN ALTERNATE BINDING SITE.
5fpo STRUCTURE OF BACTERIAL DNA LIGASE WITH SMALL-MOLECULE LIGAND 1H-INDAZOL-7-AMINE (AT4213) IN AN ALTERNATE BINDING SITE.
5fpr STRUCTURE OF BACTERIAL DNA LIGASE WITH SMALL-MOLECULE LIGAND PYRIMIDIN-2-AMINE (AT371) IN AN ALTERNATE BINDING SITE.
5fps STRUCTURE OF HEPATITIS C VIRUS (HCV) FULL-LENGTH NS3 COMPLEX WITH SMALL-MOLECULE LIGAND 3-AMINOBENZENE-1,2 -DICARBOXYLIC ACID (AT1246) IN AN ALTERNATE BINDING SITE.
5fpt STRUCTURE OF HEPATITIS C VIRUS (HCV) FULL-LENGTH NS3 COMPLEX WITH SMALL-MOLECULE LIGAND 2-(1-METHYL-1H- INDOL-3-YL)ACETIC ACID (AT3437) IN AN ALTERNATE BINDING SITE.