4MK8 - JenaLib

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Title :   HEPATITIS C VIRUS POLYMERASE NS5B GENOTYPE 1B (BK) IN COMPLEX WITH INHIBITOR 4 (N-(4-{2-[3-TERT-BUTYL-2-METHOXY-5-(2-OXO-1,2-DIHYDROPYRIDIN-3-YL)PHENYL]ETHYL}PHENYL)METHANESULFONAMIDE)

Authors :   S. F. Harris, A. Wong

Date :   04 Sep 13 (Deposition) - 09 Oct 13 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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

Keywords :   Polymerase, Transferase, Ns5B, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. C. Schoenfeld, D. L. Bourdet, K. A. Brameld, E. Chin, J. De Vicente, A. Fung, S. F. Harris, E. K. Lee, S. Le Pogam, V. Leveque, J. Li, A. S. Lui I. Najera, S. Rajyaguru, M. Sangi, S. Steiner, F. X. Talamas, J. P. Taygerly, J. Zhao
Discovery Of A Novel Series Of Potent Non-Nucleoside Inhibitors Of Hepatitis C Virus Ns5B.
J. Med. Chem. V. 56 8163 2013
PubMed-ID: 24069953 | Reference-DOI: 10.1021/JM401266K

Molecule 1 - RNA-DIRECTED RNA POLYMERASE
	Chains	:	A, B
	EC Number	:	2.7.7.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 2421-2989
	Gene	:	NS5B
	Organism Common	:	HCV
	Organism Scientific	:	HEPATITIS C VIRUS
	Organism Taxid	:	11105
	Strain	:	1B BK

		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, 6)

No.	Name	Count	Type	Full Name
1	28Q	2	Ligand/Ion	N-(4-{2-[3-TERT-BUTYL-2-METHOXY-5-(2-OXO-1,2-DIHYDROPYRIDIN-3-YL)PHENYL]ETHYL}PHENYL)METHANESULFONAMIDE
2	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	28Q	1	Ligand/Ion	N-(4-{2-[3-TERT-BUTYL-2-METHOXY-5-(2-OXO-1,2-DIHYDROPYRIDIN-3-YL)PHENYL]ETHYL}PHENYL)METHANESULFONAMIDE
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	28Q	1	Ligand/Ion	N-(4-{2-[3-TERT-BUTYL-2-METHOXY-5-(2-OXO-1,2-DIHYDROPYRIDIN-3-YL)PHENYL]ETHYL}PHENYL)METHANESULFONAMIDE
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:200 , LEU A:204 , VAL A:321 , ILE A:363 , SER A:365 , SER A:368 , LEU A:384	BINDING SITE FOR RESIDUE DMS A 601
2	AC2	SOFTWARE	SER A:288 , ASN A:291 , ASN A:316 , GLY A:317 , ASP A:318 , ASP A:319 , SER A:368 , GLY A:410 , ASN A:411 , MET A:414 , GLN A:446 , ILE A:447 , TYR A:448 , SER A:556	BINDING SITE FOR RESIDUE 28Q A 602
3	AC3	SOFTWARE	ARG B:200 , LEU B:204 , VAL B:321 , ILE B:363 , SER B:365 , SER B:368	BINDING SITE FOR RESIDUE DMS B 601
4	AC4	SOFTWARE	ARG A:401 , HIS A:402 , GLN B:184	BINDING SITE FOR RESIDUE DMS B 602
5	AC5	SOFTWARE	GLU B:143 , VAL B:144 , ARG B:394 , GLU B:398	BINDING SITE FOR RESIDUE GOL B 603
6	AC6	SOFTWARE	PHE B:193 , ARG B:200 , SER B:288 , ASN B:291 , ASN B:316 , GLY B:317 , ASP B:318 , ASP B:319 , SER B:368 , GLY B:410 , ASN B:411 , MET B:414 , TYR B:415 , GLN B:446 , ILE B:447 , TYR B:448 , SER B:556	BINDING SITE FOR RESIDUE 28Q B 604

Asymmetric Unit

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

(no "Cis Peptide Bond" information available for 4MK8)

(no "SAP(SNP)/Variant" information available for 4MK8)

(no "PROSITE Motif" information available for 4MK8)

(no "Exon" information available for 4MK8)

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:557
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4mk8a_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...................hhhhhh.hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mk8 A   1 HMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDVRNLSSKAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQRKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIPAASRLDLSGWFVAGYSGGDIYH 562
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       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       
                                                                                                                                                                             148|                                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                                                                              154

Chain B from PDB  Type:PROTEIN  Length:557
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4mk8b_ B: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...................hhhhhh.hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mk8 B   1 HMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDVRNLSSKAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQRKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIPAASRLDLSGWFVAGYSGGDIYH 562
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       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       
                                                                                                                                                                             148|                                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                                                                              154

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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	d4mk8a_	A:
1b	d4mk8b_	B:

(no "CATH Domain" information available for 4MK8)

(no "Pfam Domain" information available for 4MK8)

Asymmetric Unit(hide GO term definitions)

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	Cis Peptide Bonds
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Biological Units
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	2.7.7.48
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (73, 73)

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