4JVQ - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HCV NS5B POLYMERASE IN COMPLEX WITH COMPOUND 9

Authors :   R. Coulombe

Date :   26 Mar 13 (Deposition) - 05 Feb 14 (Release) - 26 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. R. Laplante, P. Forgione, C. Boucher, R. Coulombe, J. Gillard, O. Hucke, A. Jakalian, M. A. Joly, G. Kukolj, C. Lemke, R. Mccollum, S. Titolo, P. L. Beaulieu, T. Stammers
Enantiomeric Atropisomers Inhibit Hcv Polymerase And/Or Hiv Matrix: Characterizing Hindered Bond Rotations And Target Selectivity.
J. Med. Chem. V. 57 1944 2014
PubMed-ID: 24024973 | Reference-DOI: 10.1021/JM401202A

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	1ML	2	Ligand/Ion	5-{4-[(4-METHOXYBENZOYL)AMINO]PHENOXY}-2-{[(TRANS-4-METHYLCYCLOHEXYL)CARBONYL](PROPAN-2-YL)AMINO}BENZOICACID
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	1ML	1	Ligand/Ion	5-{4-[(4-METHOXYBENZOYL)AMINO]PHENOXY}-2-{[(TRANS-4-METHYLCYCLOHEXYL)CARBONYL](PROPAN-2-YL)AMINO}BENZOICACID
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	1ML	1	Ligand/Ion	5-{4-[(4-METHOXYBENZOYL)AMINO]PHENOXY}-2-{[(TRANS-4-METHYLCYCLOHEXYL)CARBONYL](PROPAN-2-YL)AMINO}BENZOICACID
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	ALA A:97 , ARG A:168 , HOH A:3216	BINDING SITE FOR RESIDUE GOL A 3001
2	AC2	SOFTWARE	MET A:423 , HIS A:475 , SER A:476 , TYR A:477 , ILE A:482 , ARG A:490 , VAL A:494 , PRO A:496 , LEU A:497 , TRP A:528 , HOH A:3282 , HOH A:3383	BINDING SITE FOR RESIDUE 1ML A 3002
3	AC3	SOFTWARE	GLN A:194 , GLN A:199 , PHE A:551 , HOH A:3346 , HOH A:3458	BINDING SITE FOR RESIDUE MG A 3003
4	AC4	SOFTWARE	ASP A:220 , THR A:221 , HOH A:3138 , HOH A:3211 , HOH A:3305	BINDING SITE FOR RESIDUE MG A 3004
5	AC5	SOFTWARE	SER B:96 , ALA B:97 , PHE B:162 , ARG B:168 , HOH B:783 , HOH B:916	BINDING SITE FOR RESIDUE GOL B 601
6	AC6	SOFTWARE	LYS A:209 , SER A:210 , HOH A:3454 , ARG B:422 , 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 , HOH B:974	BINDING SITE FOR RESIDUE 1ML B 602
7	AC7	SOFTWARE	GLN B:194 , PHE B:551 , HOH B:827 , HOH B:859	BINDING SITE FOR RESIDUE MG B 603
8	AC8	SOFTWARE	ASP B:220 , THR B:221 , HOH B:799 , HOH B:819	BINDING SITE FOR RESIDUE MG B 604

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

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

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

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

(no "Exon" information available for 4JVQ)

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 d4jvqa_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...................hhhhh..hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..hhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jvq 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 d4jvqb_ B: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...................hhhhh......eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhh...hhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jvq 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	d4jvqa_	A:
1b	d4jvqb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		1ML	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jvq)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4jvq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	POLG_HCVJ4 \| O92972
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.7.48
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	3.4.21.98
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	3.4.22.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	3.6.1.15
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	3.6.4.13
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	POLG_HCVJ4 \| O92972
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

3mwv	APO NS5B POLYMERASE
4jty
4jtz
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 (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (79, 79)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File