3ATH

Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with four AKGs as substrates and allosteric effectors

• PDB DOI: https://doi.org/10.2210/pdb3ATH/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-05 Released: 2012-01-18 
• Deposition Author(s): Okada, K., Angkawidjaja, C., Koga, Y., Takano, K., Kanaya, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Characterization of kynurenine aminotransferase from hyperthermophilic archaeon: enzymatic activity for conversion to kynurenic acid is allosterically regulated by alpha-ketoglutaric acid cooperatively with kynurenine

Okada, K., Angkawidjaja, C., Koga, Y., Takano, K., Kanaya, Y.

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)

Macromolecule Content

• Total Structure Weight: 103.4 kDa 
• Atom Count: 7,192 
• Modelled Residue Count: 808 
• Deposited Residue Count: 896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH0207	A, B [auth C]	448	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH0207 EC: 2.6.1.7
UniProt
Find proteins for O57946 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57946  Go to UniProtKB:  O57946

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], F [auth C]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
AKG	D [auth A], E [auth A], G [auth C], H [auth C]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.817	α = 90
b = 70.989	β = 89.998
c = 136.816	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Okada, K., Angkawidjaja, C., Koga, Y., Takano, K., Kanaya, S.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description