1JRP

Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus

Structural Biology Knowledgebase: 1JRP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 1JRP

Classification: OXIDOREDUCTASE

Total Structure Weight: 536849.25

Macromolecule Entities
Molecule Chains Length Organism Details
xanthine dehydrogenase, chain A A, C, E, G 462 Rhodobacter capsulatus EC#: 1.17.1.4 IUBMB
Fragment: chain A, residues 1-462
Gene Name(s): xdhA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
xanthine dehydrogenase, chain B B, D, F, H 777 Rhodobacter capsulatus EC#: 1.17.1.4 IUBMB
Fragment: chain B, residues 1-777
Mutation: G772R
Gene Name(s): xdhB
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, C, E, G FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MTE
Query on MTE

B, D, F, H 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

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

B, D, F, H DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
141
Query on 141

B, D, F, H Oxypurinol
Alloxanthine (Synonym)
C5 H4 N4 O2
HXNFUBHNUDHIGC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B, D, F, H CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.193
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 92.62 α = 109.59
b = 140.73 β = 105.84
c = 157.66 γ = 101.25

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-08-14
  • Released Date: 2002-01-11
  • Deposition author(s): Truglio, J.J., Theis, K., Leimkuhler, S., Rappa, R., Rajagopalan, K.V., Kisker, C.

Revision History

  • 2015-04-22
    Type: Non-polymer description | Details: --
  • 2014-09-10
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4