6ABU

Rat Xanthine oxidoreductase, NAD bound form

PDB DOI: https://doi.org/10.2210/pdb6ABU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rattus norvegicus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2018-07-24 Released: 2019-07-31
Deposition Author(s): Okamoto, K., Kawaguchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.237
R-Value Work: 0.199
R-Value Observed: 0.201

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Rat Xanthine oxidoreductase, NAD bound form

Okamoto, K., Kawaguchi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 296.89 kDa
Atom Count: 21,843
Modelled Residue Count: 2,595
Deposited Residue Count: 2,662
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthine dehydrogenase/oxidase	A, B	1,331	Rattus norvegicus	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 P22985 (Rattus norvegicus) Explore P22985 Go to UniProtKB: P22985
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22985
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	F [auth A], G [auth A], I [auth B], J [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]
URC Query on URC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B]	D [auth A], L [auth B]	URIC ACID C₅ H₄ N₄ O₃ LEHOTFFKMJEONL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B]	E [auth A], M [auth B]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.237
R-Value Work: 0.199
R-Value Observed: 0.201
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.353	α = 90
b = 137.663	β = 90
c = 221.969	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-31

Deposition Author(s):

Okamoto, K.

Kawaguchi, Y.

Funding Organization	Location	Grant Number
	Japan	15H04702

Revision History (Full details and data files)

Version 1.0: 2019-07-31
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description