2QX4

Crystal Structure of Quinone Reductase II

Structural Biology Knowledgebase: 2QX4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2QX4

Classification: oxidoreductase

Total Structure Weight: 53865.50

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 3 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ML1
Query on ML1

A, B N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide
Melatonin (Synonym)
C13 H16 N2 O2
DRLFMBDRBRZALE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ML1 IC50: 64.57 - 11300 nM (99) BindingDB
Ki: 28 - 57 nM (99) BindingDB
ΔG: -33.7 kJ/mol (99) BindingDB
-TΔS: 10 kJ/mol (99) BindingDB

Kd: 1400 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.186
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.58 α = 90.00
b = 83.62 β = 90.00
c = 106.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

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

Revision History

  • 2013-03-13
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4