2QX8

Crystal Structure of Quinone Reductase II

Structural Biology Knowledgebase: 2QX8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 2QX8

Classification: oxidoreductase

Total Structure Weight: 54372.39

Macromolecule Entities
Molecule Chains Length Organism Details
Ribosyldihydronicotinamide dehydrogenase [quinone] A, B 230 Homo sapiens EC#: 1.10.5.1 IUBMB
Gene Name(s): NQO2 Gene View NMOR2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

A, B FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ML2
Query on ML2

A, B N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide
C13 H15 I N2 O2
FJDDSMSDZHURBJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ML2 IC50: 1100 nM (99) BindingDB
Ki: 6.5 nM (99) BindingDB
ΔG: -35.5 kJ/mol (99) BindingDB
-TΔS: -2.7 kJ/mol (99) BindingDB

Kd: 700 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.211
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.60 α = 90.00
b = 83.32 β = 90.00
c = 106.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-08-10
  • Released Date: 2008-09-02
  • Deposition author(s): Calamini, B., Santarsiero, B.D., Boutin, J.A., Mesecar, A.D.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4