5E3K

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid

Filippova, E.V.Minasov, G.Flores, K.Le, H.V.Silverman, R.B.McLeod, R.L.Anderson, W.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase
A, B
441Toxoplasma gondii ME49Mutation(s): 0 
Gene Names: TGME49_269110
EC: 2.6.1.13
UniProt
Find proteins for S8EY38 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore S8EY38 
Go to UniProtKB:  S8EY38
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS8EY38
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5JV
Query on 5JV

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid
C13 H17 N2 O7 P
HRCALJQKZAULQS-MKMNVTDBSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A],
I [auth A],
Q [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CO3
Query on CO3

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B],
P [auth B]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/M35E3K
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.328α = 100.72
b = 61.524β = 92.96
c = 63.555γ = 108.18
Software Package:
Software NamePurpose
BLU-MAXdata collection
HKL-3000data scaling
PHASERphasing
Cootmodel building
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description