3E2Z

Crystal structure of mouse kynurenine aminotransferase III in complex with kynurenine

PDB DOI: https://doi.org/10.2210/pdb3E2Z/pdb

Classification: TRANSFERASE, LYASE
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2008-08-06 Released: 2008-12-30
Deposition Author(s): Han, Q., Robinson, R., Cai, T., Tagle, D.A., Li, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.237
R-Value Work: 0.192
R-Value Observed: 0.194

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5VER

Literature

Correction for Han et al., "Biochemical and Structural Properties of Mouse Kynurenine Aminotransferase III".

Han, Q., Robinson, H., Cai, T., Tagle, D.A., Li, J.

(2018) Mol Cell Biol 38

PubMed: 29712768 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/MCB.00099-18
Primary Citation of Related Structures:
3E2F, 3E2Y, 3E2Z

Organizational Affiliation

Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061.

Macromolecule Content

Total Structure Weight: 93.71 kDa
Atom Count: 6,674
Modelled Residue Count: 820
Deposited Residue Count: 820
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kynurenine-oxoglutarate transaminase 3	A	410	Mus musculus	Mutation(s): 0 Gene Names: Ccbl2, Kat3 EC: 2.6.1.7 (PDB Primary Data), 4.4.1.13 (PDB Primary Data), 2.6.1.63 (UniProt)
UniProt
Find proteins for Q71RI9 (Mus musculus) Explore Q71RI9 Go to UniProtKB: Q71RI9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q71RI9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kynurenine-oxoglutarate transaminase 3	B	410	Mus musculus	Mutation(s): 0 Gene Names: Ccbl2, Kat3 EC: 4.4.1.13 (UniProt), 2.6.1.63 (UniProt), 2.6.1.7 (UniProt)
UniProt
Find proteins for Q71RI9 (Mus musculus) Explore Q71RI9 Go to UniProtKB: Q71RI9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q71RI9
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 F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
KYN Query on KYN Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid C₁₀ H₁₂ N₂ O₃ YGPSJZOEDVAXAB-QMMMGPOBSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.237
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.49	α = 90
b = 91.49	β = 90
c = 233.501	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-12-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2018-08-01
Changes: Advisory, Data collection, Database references
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection