5UJ2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS AND DELTA8 NETA HAIRPOIN LOOP DELETION IN COMPLEX WITH GS-639476 (DIPHSOHATE VERSION OF GS-9813), MN2+ AND SYMMETRICAL PRIMER TEMPLATE 5'-AUAAAUUU

Authors :   T. E. Edwards, D. Fox Iii, T. C. Appleby, E. Murakami, A. Rey, M. E. Mcgra

Date :   16 Jan 17 (Deposition) - 22 Mar 17 (Release) - 12 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,P,T

Keywords :   Hcv, Viral, Ns5B, Rdrp, Resistance Mutation, Sofosbuvir, Sovaldi, Virunon, Gs7977-Dp, Gs-639476, Template, Primer, Immune System-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. A. Kirschberg, S. Metobo, M. O. Clarke, V. Aktoudianakis, D. Babusis, O. Barauskas, G. Birkus, T. Butler, D. Byun, G. Chin, E. Doerffler, T. E. Edwards, M. Fenaux, R. Lee, W. Lew, M. R. Mish, E. Murakami, Y. Park, N. H. Squires, N. Tirunagari, T. Wang, M. Whitcomb, J. Xu, H. Yang, H. Ye, L. Zhang, T. C. Appleby, J. Y. Feng, A. S. Ray, A. Cho, C. U. Kim
Discovery Of A 2'-Fluoro-2'-C-Methyl C-Nucleotide Hcv Polymerase Inhibitor And A Phosphoramidate Prodrug With Favorable Properties.
Bioorg. Med. Chem. Lett. V. 27 1840 2017
PubMed-ID: 28274633 | Reference-DOI: 10.1016/J.BMCL.2017.02.037

*Molecule 1 - RNA (5'-R(APUPAPAPAPUPUPU)-3')*
	Chains	:	T, P
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	VCID 6258
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - GENOME POLYPROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	HEPATITIS C VIRUS
	Organism Taxid	:	11103

		1	2	3
Asymmetric/Biological Unit	:	A	P	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	8B4	1	Ligand/Ion	(1S)-1-(4-AMINOIMIDAZO[2,1-F][1,2,4]TRIAZIN-7-YL)-1,4-ANHYDRO-2-DEOXY-2-FLUORO-5-O-[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]-2-METHYL-D-RIBITOL
2	CL	1	Ligand/Ion	CHLORIDE ION
3	MN	3	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:220 , ASP A:318 , ASP A:319 , MN A:601 , U P:8 , 8B4 P:602 , HOH P:702	binding site for residue MN P 601
2	AC2	SOFTWARE	ARG A:158 , ASP A:220 , THR A:221 , HIS A:223 , PHE A:224 , ASP A:225 , SER A:282 , ASN A:291 , ASP A:318 , MN A:601 , U P:8 , MN P:601 , HOH P:701 , HOH P:702 , U T:2 , A T:3	binding site for residue 8B4 P 602
3	AC3	SOFTWARE	ASP A:220 , THR A:221 , ASP A:318 , MN P:601 , 8B4 P:602 , HOH P:701	binding site for residue MN A 601
4	AC4	SOFTWARE	GLU A:237 , HIS A:254	binding site for residue MN A 602
5	AC5	SOFTWARE	GLY A:375 , PRO A:376 , ARG A:377 , GLY A:378 , ARG A:379	binding site for residue CL A 603

(no "SS Bond" information available for 5UJ2)

(no "Cis Peptide Bond" information available for 5UJ2)

(no "SAP(SNP)/Variant" information available for 5UJ2)

(no "PROSITE Motif" information available for 5UJ2)

(no "Exon" information available for 5UJ2)

Asymmetric/Biological 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:534
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..........................hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee...eee.hhhhh......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeee.....eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhh.......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5uj2 A   0 SSMSYSWTGALITPCGPEEEKLPINPLSNSLLRYHNKVYCTTSKSASQRAKKVTFDRTQVLDAHYDSVLKDIKLAASKVSARLLTLQQACQLTPPHSARSKYGFGAKEVRSLSGRAVNHIKSVWKDLLEDPQTPIPTTIMAKNEVFCVDPAKGGKKPARLIVYPDLGVRVCEKMALYDITQKLPQAVMGASYGFQYSPAQRVEYLLKAWAEKKDPMGFSYDTRHFDSTVTERDIRTEESIYQACSLPEEARTAIHSLTERLYVGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCYVKALAACKAAGIVAPTMLVCGDDLIVISESQGTEEDERNLRAFTEAMTRYSAPPGDPPRPEYDLELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLGNIIQYAPTIWVRMVLMTHFFSILMVQDTLDQNLYGVNPLDLPAIIERLHGLDAFSMHTYSHHELTRVASALRKLGAPPLRVWKSRARAVRASLISRGGKAAVCGRYLFNWAVKTKLKLTPLPE 541
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439     ||457       467       477       487       497       507       517       527       537    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       445|                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        454

Chain P from PDB  Type:DNA/RNA  Length:6
                                      
                 5uj2 P   3 AAAUUU   8

Chain T from PDB  Type:DNA/RNA  Length:8
                                        
                 5uj2 T   1 AUAAAUUU   8

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 '\|'

(no "SCOP Domain" information available for 5UJ2)

(no "CATH Domain" information available for 5UJ2)

(no "Pfam Domain" information available for 5UJ2)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5uj2)

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4wtd	HCV POLYMERASE TERNARY STRUCTURE WITH ADP
4wtg	HCV POLYMERASE TERNARY STRUCTURE WITH DIPHOSPHATE VERSION OF SOFOSBUVIR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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