1GBN

HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Human ornithine aminotransferase complexed with L-canaline and gabaculine: structural basis for substrate recognition.

Shah, S.A.Shen, B.W.Brunger, A.T.

(1997) Structure 5: 1067-1075

  • Primary Citation of Related Structures:  2CAN

  • PubMed Abstract: 
  • Ornithine aminotransferase (OAT) is a 45 kDa pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of L-ornithine and 2-oxoglutarate to glutamate-delta-semialdehyde and glutamic acid, respectively. In humans, loss of OAT functio ...

    Ornithine aminotransferase (OAT) is a 45 kDa pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of L-ornithine and 2-oxoglutarate to glutamate-delta-semialdehyde and glutamic acid, respectively. In humans, loss of OAT function causes an accumulation of ornithine that results in gyrate atrophy of the choroid and retina, a disease that progressively leads to blindness. In an effort to learn more about the structural basis of this enzyme's function, we have determined the X-ray structures of OAT in complex with two enzyme-activated suicide substrates: L-canaline, an ornithine analog, and gabaculine, an irreversible inhibitor of several related aminotransferases.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORNITHINE AMINOTRANSFERASE
A, B, C
402Homo sapiensGene Names: OAT
EC: 2.6.1.13
Find proteins for P04181 (Homo sapiens)
Go to Gene View: OAT
Go to UniProtKB:  P04181
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GBC
Query on GBC

Download SDF File 
Download CCD File 
B, C
GABACULINE
C7 H11 N O2
ZCGFCFMGAXXBTD-ZCFIWIBFSA-N
 Ligand Interaction
GAB
Query on GAB

Download SDF File 
Download CCD File 
A
3-AMINOBENZOIC ACID
GABACULINE
C7 H7 N O2
XFDUHJPVQKIXHO-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.013α = 90.00
b = 115.013β = 90.00
c = 185.753γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
SCALEPACKdata scaling
X-PLORrefinement
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-03
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance