5PZL - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 2-({3-[1-(2-CYCLOPROPYLETHYL)-6-FLUORO-4-HYDROXY-2-OXO-1,2-DIHYDROQUINOLIN-3-YL]-1,1-DIOXO-1,4-DIHYDRO-1LAMBDA~6~,2,4-BENZOTHIADIAZIN-7-YL}OXY)ACETAMIDE

Authors :   S. Sheriff

Date :   27 Feb 17 (Deposition) - 10 May 17 (Release) - 14 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.06

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Ns5B, Polymerase, Hcv, Fingers, Palm, Thumb, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Yeung, B. R. Beno, K. Parcella, J. A. Bender, K. A. Grant-Young, A. Nickel, P. Gunaga, P. Anjanappa, R. O. Bora, K. Selvakumar, K. Rigat Y. K. Wang, M. Liu, J. Lemm, K. Mosure, S. Sheriff, C. Wan, M. Witmer, K. Kish, U. Hanumegowda, X. Zhuo, Y. Z. Shu, D. Parker, R. Haskell, A. Ng Q. Gao, E. Colston, J. Raybon, D. M. Grasela, K. Santone, M. Gao, N. A. Meanwell, M. Sinz, M. G. Soars, J. O. Knipe, S. B. Roberts, J. F. Kadow
Discovery Of A Hepatitis C Virus Ns5B Replicase Palm Site Allosteric Inhibitor (Bms-929075) Advanced To Phase 1 Clinical Studies.
J. Med. Chem. V. 60 4369 2017
PubMed-ID: 28430437 | Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00328

Molecule 1 - RNA-DIRECTED 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)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HCV
	Organism Scientific	:	HEPATITIS C VIRUS GENOTYPE 1B (ISOLATE CON1)
	Organism Taxid	:	333284
	Strain	:	ISOLATE CON1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	23E	2	Ligand/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
2	8XV	2	Ligand/Ion	2-({3-[1-(2-CYCLOPROPYLETHYL)-6-FLUORO-4-HYDROXY-2-OXO-1,2-DIHYDROQUINOLIN-3-YL]-1,1-DIOXO-1,4-DIHYDRO-1LAMBDA~6~,2,4-BENZOTHIADIAZIN-7-YL}OXY)ACETAMIDE
3	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	23E	1	Ligand/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
2	8XV	1	Ligand/Ion	2-({3-[1-(2-CYCLOPROPYLETHYL)-6-FLUORO-4-HYDROXY-2-OXO-1,2-DIHYDROQUINOLIN-3-YL]-1,1-DIOXO-1,4-DIHYDRO-1LAMBDA~6~,2,4-BENZOTHIADIAZIN-7-YL}OXY)ACETAMIDE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	23E	1	Ligand/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
2	8XV	1	Ligand/Ion	2-({3-[1-(2-CYCLOPROPYLETHYL)-6-FLUORO-4-HYDROXY-2-OXO-1,2-DIHYDROQUINOLIN-3-YL]-1,1-DIOXO-1,4-DIHYDRO-1LAMBDA~6~,2,4-BENZOTHIADIAZIN-7-YL}OXY)ACETAMIDE
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:392 , ALA A:396 , HIS A:428 , LEU A:492 , GLY A:493 , VAL A:494 , PRO A:495 , PRO A:496 , ARG A:498 , VAL A:499 , ARG A:503 , HOH A:706 , HOH A:963 , 23E B:601 , HOH B:870	binding site for residue 23E A 601
02	AC2	SOFTWARE	PHE A:193 , ARG A:200 , THR A:287 , ASN A:291 , CYS A:316 , GLY A:317 , ASP A:318 , CYS A:366 , SER A:368 , LEU A:384 , GLY A:410 , ASN A:411 , MET A:414 , TYR A:415 , TYR A:448 , GLY A:449 , SER A:556 , HOH A:743 , HOH A:808 , HOH A:863 , HOH A:904	binding site for residue 8XV A 602
03	AC3	SOFTWARE	SER A:84 , VAL A:85 , ARG A:120 , HOH A:708 , HOH A:784	binding site for residue SO4 A 603
04	AC4	SOFTWARE	ARG A:48 , LYS A:51 , THR A:221 , CYS A:223 , HOH A:765	binding site for residue SO4 A 604
05	AC5	SOFTWARE	HIS A:374 , SER A:476 , GLY A:516 , ARG A:517 , HOH A:718 , HOH A:893	binding site for residue SO4 A 605
06	AC6	SOFTWARE	ALA A:400 , ARG A:401 , HIS A:428 , 23E A:601 , ALA B:396 , 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:843 , HOH B:870 , HOH B:919	binding site for residue 23E B 601
07	AC7	SOFTWARE	PHE B:193 , ARG B:200 , ASN B:291 , CYS B:316 , GLY B:317 , ASP B:318 , CYS B:366 , GLY B:410 , ASN B:411 , MET B:414 , TYR B:415 , TYR B:448 , GLY B:449 , SER B:556 , HOH B:743 , HOH B:763 , HOH B:858 , HOH B:942	binding site for residue 8XV B 602
08	AC8	SOFTWARE	SER B:84 , VAL B:85 , ARG B:120 , HOH B:742	binding site for residue SO4 B 603
09	AC9	SOFTWARE	ARG B:517 , HOH B:817 , HOH B:920	binding site for residue SO4 B 604
10	AD1	SOFTWARE	SER A:1 , LYS B:379 , ARG B:380	binding site for residue SO4 B 605
11	AD2	SOFTWARE	ARG B:48 , LYS B:51 , THR B:221 , ARG B:222 , CYS B:223 , HOH B:882	binding site for residue SO4 B 606

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

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

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

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

(no "Exon" information available for 5PZL)

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
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Chain A from PDB  Type:PROTEIN  Length:551
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.........ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee.............eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh...............eee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pzl A   1 SMSYTWTGALITPCVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLSRARPRWFM 573
                                    10   ||   42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572 
                                        14|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                         37

Chain B from PDB  Type:PROTEIN  Length:545
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.........ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee.............eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhhh...............eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pzl B   1 SMSYTWTGALITPCVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLSRA 567
                                    10   ||   42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562     
                                        14|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                         37

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5PZL)

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

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

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	5pzl
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(no "Related Entries Specified in the PDB File" available for 5PZL)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (74, 74)

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