3WX9 | pdb_00003wx9

Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PMP, GLA, 4AD, 2OG, GLU and KYA

• PDB DOI: https://doi.org/10.2210/pdb3WX9/pdb

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


• Deposited: 2014-07-28 Released: 2014-09-24 
• Deposition Author(s): Okada, K., Angkawidjaja, C., Koga, Y., Kanaya, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PMP, GLA, 4AD, 2OG, GLU and KYA

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

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: 104.13 kDa 
• Atom Count: 7,447 
• Modeled 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: KAT, PH0207
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP	C [auth A], H [auth C]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
3EE	F [auth A], K [auth C]	4-(2-aminophenyl)-2,4-dioxobutanoic acid C10 H9 N O4 CAOVWYZQMPNAFJ-UHFFFAOYSA-N
KYA	L [auth C]	4-hydroxyquinoline-2-carboxylic acid C10 H7 N O3 HCZHHEIFKROPDY-UHFFFAOYSA-N
GLU	G [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
AKG	D [auth A], I [auth C]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
G9A	E [auth A], J [auth C]	(2E)-pent-2-enedioic acid C5 H6 O4 XVOUMQNXTGKGMA-OWOJBTEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.769	α = 90
b = 70.997	β = 90.02
c = 136.704	γ = 90

Software Package:

Software Name	Purpose
BL38B1	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Okada, K., Angkawidjaja, C., Koga, Y., Kanaya, S.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary