2CKJ | pdb_00002ckj

Human milk xanthine oxidoreductase

• PDB DOI: https://doi.org/10.2210/pdb2CKJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2006-04-19 Released: 2007-05-29 
• Deposition Author(s): Pearson, A.R., Godber, B.L.J., Eisenthal, R., Taylor, G.L., Harrison, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free: 
  0.258 (Depositor) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Human Milk Xanthine Dehydrogenase is Incompletely Converted to the Oxidase Form in the Absence of Proteolysis. A Structural Explanation.

Pearson, A.R., Godber, B.L.J., Eisenthal, R., Taylor, G.L., Harrison, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 591.48 kDa 
• Atom Count: 39,807 
• Modelled Residue Count: 5,119 
• Deposited Residue Count: 5,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XANTHINE OXIDOREDUCTASE	A, B, C, D	1,333	Homo sapiens	Mutation(s): 0  EC: 1.1.1.204 (PDB Primary Data), 1.2.3.2 (PDB Primary Data), 1.17.3.2 (PDB Primary Data), 1.17.1.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P47989 (Homo sapiens) Explore P47989  Go to UniProtKB:  P47989
PHAROS:  P47989 GTEx:  ENSG00000158125

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	G [auth A], K [auth B], O [auth C], S [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FES	E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
PO4	V [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	H [auth A], L [auth B], P [auth C], T [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	U [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free:  0.258 (Depositor) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.734	α = 90
b = 197.734	β = 90
c = 285.538	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Pearson, A.R., Godber, B.L.J., Eisenthal, R., Taylor, G.L., Harrison, R.

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary