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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.248 (Depositor) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

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

Coulombe, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1O9	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

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), 0.210 (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

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Coulombe, R.

Revision History  

• 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