2WRM | pdb_00002wrm

Identification of Novel Allosteric Inhibitors of Hepatitis C Virus NS5B Polymerase Thumb Domain (Site II) by Structure-Based Design

• PDB DOI: https://doi.org/10.2210/pdb2WRM/pdb

• Classification: TRANSFERASE
• Organism(s): Orthohepacivirus hominis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-01 Released: 2010-09-22 
• Deposition Author(s): Di Marco, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Identification of Novel Allosteric Inhibitors of Hepatitis C Virus Ns5B Polymerase Thumb Domain (Site II) by Structure-Based Design

Di Francesco, M.E., Di Marco, S., Summa, V.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 60.62 kDa 
• Atom Count: 4,835 
• Modeled Residue Count: 531 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-DIRECTED RNA POLYMERASE	A	536	Orthohepacivirus hominis	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK)) Explore P26663  Go to UniProtKB:  P26663

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QQ3	B [auth A], C [auth A], D [auth A]	(3R)-3-(4-METHYL-1,3-DIOXO-1,3-DIHYDRO-2H-PYRROLO[3,4-C]QUINOLIN-2-YL)HEXANOIC ACID C18 H18 N2 O4 AZYBNXOGXCANBA-LLVKDONJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.764	α = 90
b = 96.175	β = 90
c = 95.683	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Di Marco, S.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description