2DU8

Crystal structure of human D-amino acid oxidase

Structural Biology Knowledgebase: 2DU8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.223

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2DU8

Classification: OXIDOREDUCTASE

Total Structure Weight: 161715.88

Macromolecule Entities
Molecule Chains Length Organism Details
D-amino-acid oxidase A, B, G, J 347 Homo sapiens EC#: 1.4.3.3 IUBMB
Gene Name(s): DAO Gene View DAMOX
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

A, B, G, J BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FAD N/A in BindingDB
Kd: 8000 nM  BindingMOAD
N/A in PDBbind
BEZ IC50: 2089 - 65700 nM (100) BindingDB
Kd: 2200 - 9000 nM (100) BindingDB
Ki: 2000 - 10900 nM (100) BindingDB

Ki: 7000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.223
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 150.98 α = 90.00
b = 183.18 β = 90.00
c = 51.08 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-07-20
  • Released Date: 2006-11-21
  • Deposition author(s): Kawazoe, T., Tsuge, H., Fukui, K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4