5PZK - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 2-(4-FLUOROPHENYL)-N-METHYL-6-[(METHYLSULFONYL)AMINO]-5-(PROPAN-2-YLOXY)-1-BENZOFURAN-3-CARBOXAMIDE

Authors :   S. Sheriff

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

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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 (5, 21)

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	2N5	2	Ligand/Ion	2-(4-FLUOROPHENYL)-N-METHYL-6-[(METHYLSULFONYL)AMINO]-5-(PROPAN-2-YLOXY)-1-BENZOFURAN-3-CARBOXAMIDE
3	GOL	4	Ligand/Ion	GLYCEROL
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 1 (5, 11)

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	2N5	1	Ligand/Ion	2-(4-FLUOROPHENYL)-N-METHYL-6-[(METHYLSULFONYL)AMINO]-5-(PROPAN-2-YLOXY)-1-BENZOFURAN-3-CARBOXAMIDE
3	GOL	3	Ligand/Ion	GLYCEROL
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 10)

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	2N5	1	Ligand/Ion	2-(4-FLUOROPHENYL)-N-METHYL-6-[(METHYLSULFONYL)AMINO]-5-(PROPAN-2-YLOXY)-1-BENZOFURAN-3-CARBOXAMIDE
3	GOL	1	Ligand/Ion	GLYCEROL
4	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SO4	7	Ligand/Ion	SULFATE ION

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:396 , HIS A:428 , LEU A:492 , GLY A:493 , VAL A:494 , PRO A:495 , ARG A:498 , VAL A:499 , ARG A:503 , HOH A:820 , 23E B:601 , HOH B:801 , HOH B:842	binding site for residue 23E A 601
02	AC2	SOFTWARE	ARG A:200 , LEU A:204 , LEU A:314 , CYS A:316 , ASP A:319 , VAL A:321 , LEU A:360 , ILE A:363 , SER A:365 , CYS A:366 , SER A:368 , LEU A:384 , MET A:414 , TYR A:415 , TYR A:448	binding site for residue 2N5 A 602
03	AC3	SOFTWARE	HIS A:374 , ARG A:380 , GLY A:516 , ARG A:517 , HOH A:849 , HOH A:862	binding site for residue SO4 A 603
04	AC4	SOFTWARE	THR A:329 , ARG A:505 , VAL A:530 , ARG A:531 , THR A:532 , HOH A:707 , HOH A:792	binding site for residue SO4 A 604
05	AC5	SOFTWARE	ARG A:48 , LYS A:51 , ARG A:222 , CYS A:223 , HOH A:794 , HOH A:845 , HOH A:856	binding site for residue SO4 A 605
06	AC6	SOFTWARE	SER A:84 , VAL A:85 , ARG A:120	binding site for residue SO4 A 606
07	AC7	SOFTWARE	GLY A:188 , SER A:189	binding site for residue SO4 A 607
08	AC8	SOFTWARE	ASP A:244 , LEU A:245 , PRO A:247 , GOL A:610 , HOH A:775 , HOH A:836 , ASN B:231	binding site for residue GOL A 608
09	AC9	SOFTWARE	ARG A:65 , ASN A:231 , VAL A:235 , HOH A:808 , LYS B:79 , ASP B:244 , GOL B:610	binding site for residue GOL A 609
10	AD1	SOFTWARE	LYS A:79 , ASP A:244 , GOL A:608 , ARG B:65 , LEU B:68 , ASN B:231 , VAL B:235 , HOH B:852	binding site for residue GOL A 610
11	AD2	SOFTWARE	LYS A:209 , GLU A:361 , TYR A:382 , GLU A:437	binding site for residue PG4 A 611
12	AD3	SOFTWARE	ALA A:400 , ARG A:401 , 23E A:601 , ALA B:396 , HIS B:428 , LEU B:492 , GLY B:493 , VAL B:494 , PRO B:495 , ARG B:498 , VAL B:499 , ARG B:503 , HOH B:842	binding site for residue 23E B 601
13	AD4	SOFTWARE	PRO B:197 , ARG B:200 , LEU B:204 , LEU B:314 , CYS B:316 , ASP B:319 , VAL B:321 , LEU B:360 , ILE B:363 , SER B:365 , CYS B:366 , SER B:368 , LEU B:384 , MET B:414 , TYR B:415 , TYR B:448	binding site for residue 2N5 B 602
14	AD5	SOFTWARE	ARG B:48 , LYS B:51 , ARG B:222 , CYS B:223	binding site for residue SO4 B 603
15	AD6	SOFTWARE	GLU B:361 , SER B:478 , PRO B:479 , GLY B:480 , GLU B:481 , HOH B:722	binding site for residue SO4 B 604
16	AD7	SOFTWARE	ARG B:505 , VAL B:530 , ARG B:531 , THR B:532	binding site for residue SO4 B 605
17	AD8	SOFTWARE	HIS B:475 , SER B:476 , HOH B:847	binding site for residue SO4 B 606
18	AD9	SOFTWARE	GLY B:188 , SER B:189	binding site for residue SO4 B 607
19	AE1	SOFTWARE	GLY B:516 , ARG B:517 , HOH B:881	binding site for residue SO4 B 608
20	AE2	SOFTWARE	SER B:84 , VAL B:85 , GLU B:86 , ARG B:120	binding site for residue SO4 B 609
21	AE3	SOFTWARE	ASN A:231 , GOL A:609 , ASP B:244 , LEU B:245 , PRO B:247 , HOH B:729 , HOH B:794	binding site for residue GOL B 610

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

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

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

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

(no "Exon" information available for 5PZK)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:541
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.........ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee.............eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh...............ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pzk A   1 SMSYTWTGALITPCVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHS 563
                                    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

Chain B from PDB  Type:PROTEIN  Length:542
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               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..eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh...............eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pzk B   1 SMSYTWTGALITPCVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSL 564
                                    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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	5pzk
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Description

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Ligands, Modified Residues, Ions (5, 21)

Sites (21, 21)

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