4QOD | pdb_00004qod

The value crystal structure of apo quinone reductase 2 at 1.35A

• PDB DOI: https://doi.org/10.2210/pdb4QOD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-06-20 Released: 2015-07-01 
• Deposition Author(s): Serriere, J., Boutin, J.A., Isabet, T., Antoine, M., Ferry, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.191 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

The value crystal structure of apo quinone reductase 2 at 1.35A

Serriere, J., Boutin, J.A., Isabet, T., Antoine, M., Ferry, G.

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: 52.64 kDa 
• Atom Count: 4,129 
• Modeled Residue Count: 458 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosyldihydronicotinamide dehydrogenase [quinone]	A, B	231	Homo sapiens	Mutation(s): 1  Gene Names: NQO2, NMOR2 EC: 1.10.99.2 (PDB Primary Data), 1.10.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16083 (Homo sapiens) Explore P16083  Go to UniProtKB:  P16083
PHAROS:  P16083 GTEx:  ENSG00000124588

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.191 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.12	α = 90
b = 83.2	β = 90
c = 106.54	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Serriere, J., Boutin, J.A., Isabet, T., Antoine, M., Ferry, G.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description