3AV7 | pdb_00003av7

Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PMP, KYN as substrates and KYA as products

PDB DOI: https://doi.org/10.2210/pdb3AV7/pdb

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

Deposited: 2011-02-23 Released: 2012-03-07
Deposition Author(s): Okada, K., Angkawidjaja, C., Koga, Y., Takano, K., Kanaya, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.238 (Depositor), 0.236 (DCC)
R-Value Work:
0.176 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural insight into kynurenic acid excretion mechanisms of kynurenine aminotransferase in the hyperthermophilic archaeon Pyrococcus horikoshii

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

To be published.

Macromolecule Content

Total Structure Weight: 103.62 kDa
Atom Count: 7,139
Modeled Residue Count: 808
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O57946
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMP Query on PMP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth C] MOL2 format, chain C [auth A] MOL2 format, chain F [auth C] mmCIF format, chain C [auth A] mmCIF format, chain F [auth C]	C [auth A], F [auth C]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth C] Interactions & Density Focus chain C [auth A] Focus chain F [auth C]
KYN Query on KYN Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain D [auth A] MOL2 format, chain G [auth C] MOL2 format, chain D [auth A] mmCIF format, chain G [auth C] mmCIF format, chain D [auth A]	D [auth A], G [auth C]	(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid C₁₀ H₁₂ N₂ O₃ YGPSJZOEDVAXAB-QMMMGPOBSA-N		Interactions Focus chain D [auth A] Focus chain G [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth C]
KYA Query on KYA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C]	E [auth A], H [auth C]	4-hydroxyquinoline-2-carboxylic acid C₁₀ H₇ N O₃ HCZHHEIFKROPDY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.238 (Depositor), 0.236 (DCC)
R-Value Work: 0.176 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.619	α = 90
b = 136.529	β = 100.71
c = 55.612	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-03-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-03-07
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary