1N5X | pdb_00001n5x

Xanthine Dehydrogenase from Bovine Milk with Inhibitor TEI-6720 Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.275 (Depositor) 
  • R-Value Work: 
    0.244 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1N5X

This is version 1.4 of the entry. See complete history

Literature

An Extremely Potent Inhibitor of Xanthine Oxidoreductase: Crystal Structure of the Enzyme-Inhibitor Complex and Mechanism of Inhibition

Okamoto, K.Eger, B.T.Nishino, T.Kondo, S.Pai, E.F.Nishino, T.

(2003) J Biological Chem 278: 1848-1855

  • DOI: https://doi.org/10.1074/jbc.M208307200
  • Primary Citation Related Structures: 
    1N5X

  • PubMed Abstract: 

    TEI-6720 (2-(3-cyano-4-isobutoxyphenyl)-4-methyl-5-thiazolecarboxylic acid) is an extremely potent inhibitor of xanthine oxidoreductase. Steady state kinetics measurements exhibit mixed type inhibition with K(i) and K(i)' values of 1.2 +/- 0.05 x 10(-10) m and 9 +/- 0.05 x 10(-10) m, respectively. Fluorescence-monitored titration experiments showed that TEI-6720 bound very tightly to both the active and the inactive desulfo-form of the enzyme. The dissociation constant determined for the desulfo-form was 2 +/- 0.03 x 10(-9) m; for the active form, the corresponding number was too low to allow accurate measurements. The crystal structure of the active sulfo-form of milk xanthine dehydrogenase complexed with TEI-6720 and determined at 2.8-A resolution revealed the inhibitor molecule bound in a long, narrow channel leading to the molybdenum-pterin active site of the enzyme. It filled up most of the channel and the immediate environment of the cofactor, very effectively inhibiting the activity of the enzyme through the prevention of substrate binding. Although the inhibitor did not directly coordinate to the molybdenum ion, numerous hydrogen bonds as well as hydrophobic interactions with the protein matrix were observed, most of which are also used in substrate recognition.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-0022, Japan.

Macromolecule Content 

  • Total Structure Weight: 297.74 kDa 
  • Atom Count: 20,268 
  • Modeled Residue Count: 2,580 
  • Deposited Residue Count: 2,662 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Xanthine Dehydrogenase
A, B
1,331Bos taurusMutation(s): 0 
EC: 1.1.1.204 (PDB Primary Data), 1.17.1.4 (UniProt), 1.17.3.2 (UniProt)
UniProt
Find proteins for P80457 (Bos taurus)
Explore P80457 
Go to UniProtKB:  P80457
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80457
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
G [auth A],
M [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MTE

Query on MTE



Download:Ideal Coordinates CCD File
E [auth A],
K [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
TEI

Query on TEI



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B]
2-(3-CYANO-4-ISOBUTOXY-PHENYL)-4-METHYL-5-THIAZOLE-CARBOXYLIC ACID
C16 H16 N2 O3 S
BQSJTQLCZDPROO-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
I [auth B],
J [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MOS

Query on MOS



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.275 (Depositor) 
  • R-Value Work:  0.244 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.269α = 90
b = 124.659β = 90.99
c = 147.325γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-05-08
    Changes: Other
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description