4Y0I | pdb_00004y0i

GABA-aminotransferase inactivated by conformationally-restricted inactivator

• PDB DOI: https://doi.org/10.2210/pdb4Y0I/pdb

• Classification: TRANSFERASE
• Organism(s): Sus scrofa
• Expression System: Sus barbatus
• Mutation(s): No 


• Deposited: 2015-02-06 Released: 2016-02-17 
• Deposition Author(s): Wu, R., Sanishvili, R., Lee, H.V., Dustin, D.H., Emma, D., Neil, K., Silverman, R.B., Liu, D.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

GABA-aminotransferase inactivated by conformationally-restricted inactivator

Lee, H.V., Dustin, D.H., Wu, R., Emma, D., Sanishvili, R., Liu, D., Neil, K., Silverman, R.B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 211 kDa 
• Atom Count: 17,146 
• Modeled Residue Count: 1,844 
• Deposited Residue Count: 1,844 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-aminobutyrate aminotransferase, mitochondrial	A, B, C, D	461	Sus scrofa	Mutation(s): 0  Gene Names: ABAT, GABAT EC: 2.6.1.19 (PDB Primary Data), 2.6.1.22 (PDB Primary Data)
UniProt
Find proteins for P80147 (Sus scrofa) Explore P80147  Go to UniProtKB:  P80147

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PSZ	E [auth A], H [auth B], K [auth C], L [auth D]	4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]THIOPHENE-2-CARBOXYLIC ACID C13 H15 N2 O7 P S SUKBSASAEROGCJ-UHFFFAOYSA-N
FES	F [auth A], J [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL	G [auth B], I [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.483	α = 90
b = 226.755	β = 108.79
c = 71.425	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Wu, R., Sanishvili, R., Lee, H.V., Dustin, D.H., Emma, D., Neil, K., Silverman, R.B., Liu, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	ACB-12002

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations