2ZKU

Structure of hepatitis C virus NS5B polymerase in a new crystal form

PDB DOI: https://doi.org/10.2210/pdb2ZKU/pdb

Classification: TRANSFERASE
Organism(s): Hepatitis C virus subtype 1b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-03-31 Released: 2009-04-07
Deposition Author(s): Biswal, B.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.246
R-Value Work: 0.206
R-Value Observed: 0.206

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of Hepatitis C Virus Ns5B Polymerase in a New Crystal Form: Insights Into Oligomerisation and Allosteric Nucleotide Binding Site

Biswal, B.K., Cherney, M.M., Chan, L., Yannopoulos, C.G., Bilimoria, D., Bedard, J., James, M.N.G.

To be published.

Macromolecule Content

Total Structure Weight: 257.48 kDa
Atom Count: 19,620
Modelled Residue Count: 2,244
Deposited Residue Count: 2,304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B, C, D	576	Hepatitis C virus subtype 1b	Mutation(s): 0 Gene Names: NS5B EC: 2.7.7.48
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK)) Explore P26663 Go to UniProtKB: P26663
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26663
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D]	E [auth A] F [auth A] L [auth B] M [auth B] N [auth B] E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.246
R-Value Work: 0.206
R-Value Observed: 0.206
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.99	α = 90
b = 102.06	β = 90
c = 251.81	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Biswal, B.K.

Revision History (Full details and data files)

Version 1.0: 2009-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description