4JY0 | pdb_00004jy0

Crystal structure of hcv ns5b polymerase in complex with compound 3

PDB DOI: https://doi.org/10.2210/pdb4JY0/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Hepatitis C virus isolate HC-J4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-03-28 Released: 2014-04-23
Deposition Author(s): Coulombe, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.248 (Depositor)
R-Value Work:
0.213 (Depositor), 0.211 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Distinguishing drug binding pockets on proteins by complementary biophysical and biological methods.

Coulombe, R.

To be published.

Macromolecule Content

Total Structure Weight: 129.56 kDa
Atom Count: 9,260
Modeled Residue Count: 1,117
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	576	Hepatitis C virus isolate HC-J4	Mutation(s): 0 Gene Names: NS5B EC: 3.4.22 (PDB Primary Data), 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4)) Explore O92972 Go to UniProtKB: O92972
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O92972
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1O9 Query on 1O9 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	(4S,5R)-1-(4-tert-butylbenzoyl)-2-(2-methylpropyl)-4-pyrazin-2-yl-5-(1,3-thiazol-2-yl)-L-proline C₂₇ H₃₂ N₄ O₃ S ZQOLMKRLEPUUFO-NTOOTBGVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.248 (Depositor)
R-Value Work: 0.213 (Depositor), 0.211 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.82	α = 90
b = 107.97	β = 90
c = 133.42	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-23
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.