1WYG

Crystal Structure of a Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 1WYG

Classification: OXIDOREDUCTASE

Total Structure Weight: 148080.64

Macromolecule Entities
Molecule Chains Length Organism Details
Xanthine dehydrogenase/oxidase A 1331 Rattus norvegicus EC#: 1.17.1.4 IUBMB 1.17.3.2 IUBMB
Mutation: C535A, C992R, C1324S
Gene Name(s): Xdh
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

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

A FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SAL
Query on SAL

A 2-HYDROXYBENZOIC ACID
SALICYLIC ACID (Synonym)
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SAL Ki: 100000000 nM (86) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.203
  • Space Group: I 41 2 2

Unit Cell:

Length (Å) Angle (°)
a = 134.25 α = 90.00
b = 134.25 β = 90.00
c = 523.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-14
  • Released Date: 2005-05-31
  • Deposition author(s): Nishino, T., Okamoto, K., Kawaguchi, Y., Hori, H., Matsumura, T., Eger, B.T., Pai, E.F., Nishino, T.

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Derived calculations, Version format compliance