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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 2-[(BENZENECARBONYL)AMINO]-3-[(4-CHLOROPHENYL)METHOXY]BENZOIC ACID
 
Authors :  S. Sheriff
Date :  26 Oct 16  (Deposition) - 30 Nov 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ns5B, Polymerase, Hcv, Fingers, Palm, Thumb, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Parcella, A. Nickel, B. R. Beno, S. Sheriff, C. Wan, Y. K. Wang, S. B. Roberts, N. A. Meanwell, J. F. Kadow
Discovery And Initial Optimization Of Alkoxyanthranilic Aci Derivatives As Inhibitors Of Hcv Ns5B Polymerase.
Bioorg. Med. Chem. Lett. V. 27 295 2017
PubMed-ID: 27908764  |  Reference-DOI: 10.1016/J.BMCL.2016.11.054

(-) Compounds

Molecule 1 - NS5B RNA-DEPENDENT RNA POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2420-2992
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Strain: GENOTYPE 1B CON1 STRAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
123E2Ligand/Ion(2E)-3-(4-{[(1-{[(13-CYCLOHEXYL-6-OXO-6,7-DIHYDRO-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-YL)CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-ENOIC ACID
27HL2Ligand/Ion2-[(BENZENECARBONYL)AMINO]-3-[(4-CHLOROPHENYL)METHOXY]BENZOIC ACID
3SO410Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
123E1Ligand/Ion(2E)-3-(4-{[(1-{[(13-CYCLOHEXYL-6-OXO-6,7-DIHYDRO-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-YL)CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-ENOIC ACID
27HL1Ligand/Ion2-[(BENZENECARBONYL)AMINO]-3-[(4-CHLOROPHENYL)METHOXY]BENZOIC ACID
3SO45Ligand/IonSULFATE ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
123E1Ligand/Ion(2E)-3-(4-{[(1-{[(13-CYCLOHEXYL-6-OXO-6,7-DIHYDRO-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-YL)CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-ENOIC ACID
27HL1Ligand/Ion2-[(BENZENECARBONYL)AMINO]-3-[(4-CHLOROPHENYL)METHOXY]BENZOIC ACID
3SO45Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:392 , ALA A:395 , ALA A:396 , ILE A:424 , HIS A:428 , LEU A:492 , GLY A:493 , VAL A:494 , PRO A:495 , PRO A:496 , ARG A:498 , ARG A:503 , 23E B:601 , HOH B:723binding site for residue 23E A 601
02AC2SOFTWAREPHE A:193 , CYS A:366 , SER A:368 , LEU A:384 , GLY A:410 , ASN A:411 , MET A:414 , TYR A:415 , GLN A:446 , TYR A:448 , GLY A:449 , SER A:556binding site for residue 7HL A 602
03AC3SOFTWAREHIS A:374 , SER A:476 , GLY A:516 , ARG A:517binding site for residue SO4 A 603
04AC4SOFTWAREARG A:48 , LYS A:51 , THR A:221 , ARG A:222 , CYS A:223 , HOH A:728binding site for residue SO4 A 604
05AC5SOFTWARESER A:84 , VAL A:85 , ARG A:120 , HOH A:706binding site for residue SO4 A 605
06AC6SOFTWAREPRO A:496 , LEU A:497 , ARG A:498 , ARG A:570binding site for residue SO4 A 606
07AC7SOFTWAREGLU A:361 , SER A:371 , SER A:478 , LYS A:523 , HOH A:717binding site for residue SO4 A 607
08AC8SOFTWAREALA A:400 , HIS A:428 , 23E A:601 , LEU B:392 , ALA B:395 , ALA B:396 , ILE B:424 , HIS B:428 , LEU B:492 , GLY B:493 , VAL B:494 , PRO B:495 , PRO B:496 , ARG B:498 , VAL B:499 , ARG B:503 , HOH B:723binding site for residue 23E B 601
09AC9SOFTWAREPHE B:193 , CYS B:366 , SER B:368 , LEU B:384 , GLY B:410 , ASN B:411 , MET B:414 , TYR B:415 , GLN B:446 , TYR B:448 , GLY B:449 , SER B:556binding site for residue 7HL B 602
10AD1SOFTWAREARG B:517binding site for residue SO4 B 603
11AD2SOFTWARELYS B:51 , THR B:221 , ARG B:222 , CYS B:223binding site for residue SO4 B 604
12AD3SOFTWARESER B:367 , ARG B:386 , THR B:390 , ARG B:394binding site for residue SO4 B 605
13AD4SOFTWARESER A:1 , LYS B:379 , ARG B:380binding site for residue SO4 B 606
14AD5SOFTWARESER B:84 , VAL B:85 , ARG B:120binding site for residue SO4 B 607

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5TRH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TRH)

(-) Sequences/Alignments

Asymmetric 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:550
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee..................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............ee..............eee.ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5trh A   1 SMSYTWTGALITPCYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLSRARPRWFM 573
                                    10   ||   43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573
                                        14|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                         38                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:542
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee..................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh................eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5trh B   1 SMSYTWTGALITPCTTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLSRA 567
                                    10   ||   45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565  
                                        14|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                         40
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  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 5TRH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 74)

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  POLG_HCVCO | Q9WMX2
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        POLG_HCVCO | Q9WMX2: 1zh1 2jy0 2kwt 2kwz 3fql 3fqm 3fqq 3kn2 3kqh 3kqk 3kql 3kqn 3kqu 3q0z 3qgd 3qge 3qgf 3qgg 4nld 4u01 5e4f 5pzk 5pzl 5pzm 5pzn 5pzo 5pzp 5tri 5trj 5trk 5twn

(-) Related Entries Specified in the PDB File

5tri 5trj 5trk