3UNC

Crystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A Resolution

Structural Biology Knowledgebase: 3UNC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3UNC

Classification: OXIDOREDUCTASE

Total Structure Weight: 300015.75

Macromolecule Entities
Molecule Chains Length Organism Details
Xanthine dehydrogenase/oxidase A, B 1332 Bos taurus EC#: 1.17.1.4 IUBMB 1.17.3.2 IUBMB
Gene Name(s): XDH Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 8 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)
MTE
Query on MTE

A, B PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO- 4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA- 1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

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

A, B DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SAL
Query on SAL

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

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CO3
Query on CO3

A, B CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SAL Ki: 100000000 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.177
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 167.57 α = 90.00
b = 124.37 β = 91.02
c = 148.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-11-15
  • Released Date: 2012-05-09
  • Deposition author(s): Eger, B.T., Okamoto, K., Nishino, T., Pai, E.F.

Revision History

No revisions since initial release