3AMZ

Bovine Xanthine Oxidoreductase urate bound form

PDB DOI: https://doi.org/10.2210/pdb3AMZ/pdb

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

Deposited: 2010-08-27 Released: 2010-12-01
Deposition Author(s): Okamoto, K., Eger, B.T., Pai, E.F., Nishino, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.202
R-Value Work: 0.151
R-Value Observed: 0.153

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structures of Urate Bound Form of Xanthine Oxidoreductase: Substrate Orientation and Structure of the Key Reaction Intermediate

Okamoto, K., Kawaguchi, Y., Eger, B.T., Pai, E.F., Nishino, T.

(2010) J Am Chem Soc 132: 17080-17083

PubMed: 21077683 Search on PubMed
DOI: https://doi.org/10.1021/ja1077574
Primary Citation of Related Structures:
3AMZ, 3AN1

PubMed Abstract:
Two contradictory models have been proposed for the binding mode of the substrate xanthine to and its activation mechanism by xanthine oxidoreductase. In an effort to distinguish between the two models, we determined the crystal structures of the urate complexes of the demolybdo-form of the D428A mutant of rat xanthine oxidoreductase at 1.7 Å and of the reduced bovine milk enzyme at 2.1 Å, the latter representing a reaction intermediate. The results clearly indicate the catalytically relevant binding mode of the substrate xanthine.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyou-ku, Tokyo 113-8602, Japan.

Macromolecule Content

Total Structure Weight: 299.52 kDa
Atom Count: 22,382
Modelled Residue Count: 2,580
Deposited Residue Count: 2,664
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	1,332	Bos taurus	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80457
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 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 Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth B]	F [auth A], Q [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain Q [auth B]
NAI Query on NAI Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain R [auth B]	G [auth A], R [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain R [auth B]
MTE Query on MTE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth B] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B] mmCIF format, chain K [auth A] mmCIF format, chain U [auth B]	K [auth A], U [auth B]	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		Interactions Focus chain K [auth A] Focus chain U [auth B] Interactions & Density Focus chain K [auth A] Focus chain U [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 N [auth B] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	C [auth A], D [auth A], N [auth B], O [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain N [auth B] Focus chain O [auth B]
URC Query on URC Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] mmCIF format, chain M [auth A] mmCIF format, chain W [auth B]	M [auth A], W [auth B]	URIC ACID C₅ H₄ N₄ O₃ LEHOTFFKMJEONL-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain W [auth B] Interactions & Density Focus chain M [auth A] Focus chain W [auth B]
MOS Query on MOS Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain L [auth A] MOL2 format, chain V [auth B] MOL2 format, chain L [auth A] mmCIF format, chain V [auth B] mmCIF format, chain L [auth A]	L [auth A], V [auth B]	DIOXOTHIOMOLYBDENUM(VI) ION H Mo O₂ S BDSRWPHSAKXXRG-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain V [auth B] Interactions & Density Focus chain L [auth A] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B]	I [auth A], J [auth A], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B] mmCIF format, chain H [auth A] mmCIF format, chain S [auth B]	H [auth A], S [auth B]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain S [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B]	E [auth A], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.202
R-Value Work: 0.151
R-Value Observed: 0.153
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.211	α = 90
b = 124.53	β = 91.07
c = 148.025	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description