4JTZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF HCV NS5B POLYMERASE IN COMPLEX WITH COMPOUND 4

Authors :   R. Coulombe

Date :   24 Mar 13 (Deposition) - 03 Jul 13 (Release) - 26 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Rna-Directed Rna Polymerase, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Hucke, R. Coulombe, P. Bonneau, M. Bertrand-Laperle, C. Brochu, J. Gillard, M. A. Joly, S. Landry, O. Lepage, M. Llinas-Brunet, M. Pesant, M. Poirier, M. Poirier, G. Mckercher, M. Marquis, G. Kukolj P. L. Beaulieu, T. A. Stammers
Molecular Dynamics Simulations And Structure-Based Rational Design Lead To Allosteric Hcv Ns5B Polymerase Thumb Pocket Inhibitor With Picomolar Cellular Replicon Potency.
J. Med. Chem. V. 57 1932 2014
PubMed-ID: 23773186 | Reference-DOI: 10.1021/JM4004522

Molecule 1 - GENOME POLYPROTEIN
	Chains	:	A, B
	EC Number	:	3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET29B
	Expression System Strain	:	JM109(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RNA-DIRECTED RNA POLYMERASE, UNP RESIDUES 2420-2989
	Gene	:	NS5B
	Organism Common	:	HCV
	Organism Scientific	:	HEPATITIS C VIRUS
	Organism Taxid	:	420174
	Other Details	:	PROTEIN CONSTRUCT ID 001
	Strain	:	1BJ4
	Synonym	:	CORE PROTEIN P21, CAPSID PROTEIN C, P21, CORE PROTEIN P19, ENVELOPE GLYCOPROTEIN E1, GP32, GP35, ENVELOPE GLYCOPROTEIN E2, NS1, GP68, GP70, P7, PROTEASE NS2-3, P23, SERINE PROTEASE NS3, HEPACIVIRIN, NS3P, P70, NON-STRUCTURAL PROTEIN 4A, NS4A, P8, NON- STRUCTURAL PROTEIN 4B, NS4B, P27, NON-STRUCTURAL PROTEIN 5A, NS5A, P56, RNA-DIRECTED RNA POLYMERASE, NS5B, P68

		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, 8)

No.	Name	Count	Type	Full Name
1	1NW	2	Ligand/Ion	3-{[4-OXO-1-(2,4,6-TRIFLUOROBENZYL)-1,4-DIHYDROQUINAZOLIN-6-YL]OXY}-N-(PYRIDIN-3-YL)-2-(TRIFLUOROMETHYL)BENZAMIDE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	1NW	1	Ligand/Ion	3-{[4-OXO-1-(2,4,6-TRIFLUOROBENZYL)-1,4-DIHYDROQUINAZOLIN-6-YL]OXY}-N-(PYRIDIN-3-YL)-2-(TRIFLUOROMETHYL)BENZAMIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	1NW	1	Ligand/Ion	3-{[4-OXO-1-(2,4,6-TRIFLUOROBENZYL)-1,4-DIHYDROQUINAZOLIN-6-YL]OXY}-N-(PYRIDIN-3-YL)-2-(TRIFLUOROMETHYL)BENZAMIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:96 , ALA A:97 , ARG A:168	BINDING SITE FOR RESIDUE GOL A 3001
2	AC2	SOFTWARE	LEU A:419 , ARG A:422 , MET A:423 , LEU A:474 , HIS A:475 , SER A:476 , TYR A:477 , ILE A:482 , VAL A:485 , ALA A:486 , ARG A:490 , PRO A:496 , LEU A:497 , TRP A:528 , HOH A:3221	BINDING SITE FOR RESIDUE 1NW A 3002
3	AC3	SOFTWARE	GLN A:194 , PHE A:551 , HOH A:3270	BINDING SITE FOR RESIDUE MG A 3003
4	AC4	SOFTWARE	ASP A:220 , THR A:221 , HOH A:3130	BINDING SITE FOR RESIDUE MG A 3004
5	AC5	SOFTWARE	SER B:96 , ALA B:97 , PHE B:162	BINDING SITE FOR RESIDUE GOL B 601
6	AC6	SOFTWARE	LYS A:209 , LEU B:419 , ARG B:422 , MET B:423 , LEU B:474 , HIS B:475 , SER B:476 , TYR B:477 , ILE B:482 , ALA B:486 , LEU B:489 , ARG B:490 , VAL B:494 , PRO B:496 , LEU B:497 , TRP B:528	BINDING SITE FOR RESIDUE 1NW B 602
7	AC7	SOFTWARE	GLN B:194 , GLN B:199 , PHE B:551 , HOH B:1100	BINDING SITE FOR RESIDUE MG B 603
8	AC8	SOFTWARE	ASP B:220 , HOH B:1160	BINDING SITE FOR RESIDUE MG B 604

Asymmetric Unit

No.	Residues
1	A:303	-	A:311
2	B:303	-	B:311

(no "Cis Peptide Bond" information available for 4JTZ)

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

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

(no "Exon" information available for 4JTZ)

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:560
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jtza_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhh.hhh.eee.hhhhhhhhhhhh........hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee...eee.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh...eee......hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhh....hhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtz A   1 SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHS 563
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       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
                                                                                                                                                                              149|                                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                               153

Chain B from PDB  Type:PROTEIN  Length:560
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jtzb_ B: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..............................eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeee.......eeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhh..............hhhhhh..hhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtz B   1 SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHS 563
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       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
                                                                                                                                                                              149|                                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                               153

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: DNA/RNA polymerases (850)

Superfamily: DNA/RNA polymerases (850)

Family: RNA-dependent RNA-polymerase (253)

Protein domain: Viral RNA polymerase (148)

Hepatitis C virus [TaxId: 11103] (72)

1a	d4jtza_	A:
1b	d4jtzb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

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3mwv	APO NS5B POLYMERASE
4jtw
4jty
4ju1
4ju2
4ju3
4ju4
4ju6
4ju7
4jvq
4jy0
4jy1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (79, 79)

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Related Entries Specified in the PDB File