6ADJ | pdb_00006adj

Rat Xanthine oxidoreductase, D428E variant

PDB DOI: https://doi.org/10.2210/pdb6ADJ/pdb

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

Deposited: 2018-08-01 Released: 2019-08-07
Deposition Author(s): Okamoto, K., Kawaguchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.210 (Depositor), 0.216 (DCC)
R-Value Work:
0.167 (Depositor), 0.175 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6ADJ

Ligand Structure Quality Assessment

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

Literature

Rat Xanthine oxidoreductase, D428A variant, NAD bound form

Okamoto, K., Kawaguchi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 295.21 kDa
Atom Count: 21,477
Modeled Residue Count: 2,583
Deposited Residue Count: 2,662
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22985
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth B], H [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.210 (Depositor), 0.216 (DCC)
R-Value Work: 0.167 (Depositor), 0.175 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.836	α = 90
b = 138.665	β = 90
c = 222.463	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
	Japan	15H04702

Revision History (Full details and data files)

Version 1.0: 2019-08-07
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.