8J79 | pdb_00008j79

Bovine Xanthine Oxidoreductase Crystallized with oxypurinol

PDB DOI: https://doi.org/10.2210/pdb8J79/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Expression System: Bos taurus
Mutation(s): No

Deposited: 2023-04-27 Released: 2023-05-24
Deposition Author(s): Okamoto, K., Sekine, M.
Funding Organization(s): Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.197 (Depositor), 0.204 (DCC)
R-Value Work:
0.163 (Depositor), 0.171 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Bovine Xanthine Oxidoreductase Crystallized with oxypurinol

Okamoto, K., Sekine, M.

To be published.

Macromolecule Content

Total Structure Weight: 298.46 kDa
Atom Count: 22,065
Modeled Residue Count: 2,573
Deposited Residue Count: 2,664
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthine dehydrogenase/oxidase	A, B	1,332	Bos taurus	Mutation(s): 0 Gene Names: XDH EC: 1.17.1.4 (PDB Primary Data), 1.17.3.2 (PDB Primary Data)
UniProt
Find proteins for P80457 (Bos taurus) Explore P80457 Go to UniProtKB: P80457
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80457
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B]	E [auth A], O [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain O [auth B]
ZXF Query on ZXF Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain X [auth B] MOL2 format, chain L [auth A] MOL2 format, chain X [auth B] mmCIF format, chain L [auth A] mmCIF format, chain X [auth B]	L [auth A], X [auth B]	Molybdopterin hydoxy-oxo-thiol-molybdenum C₁₀ H₁₄ Mo N₅ O₈ P S₃ KIFQXVGEKPMGCB-BKZHXLINSA-J		Interactions Focus chain L [auth A] Focus chain X [auth B] Interactions & Density Focus chain L [auth A] Focus chain X [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	C [auth A], D [auth A], M [auth B], N [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B]
141 Query on 141 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] mmCIF format, chain I [auth A] mmCIF format, chain S [auth B]	I [auth A], S [auth B]	Oxypurinol C₅ H₄ N₄ O₂ HXNFUBHNUDHIGC-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain S [auth B] Interactions & Density Focus chain I [auth A] Focus chain S [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	J [auth A] K [auth A] T [auth B] U [auth B] V [auth B] J [auth A], K [auth A], T [auth B], U [auth B], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain P [auth B]	F [auth A], P [auth B]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain P [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	G [auth A], H [auth A], Q [auth B], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.197 (Depositor), 0.204 (DCC)
R-Value Work: 0.163 (Depositor), 0.171 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.678	α = 90
b = 123.47	β = 90.89
c = 150.059	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-24

Deposition Author(s):

Okamoto, K.

Sekine, M.

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	15H04702

Revision History (Full details and data files)

Version 1.0: 2023-05-24
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection
Version 2.0: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary