3II0

Crystal structure of human Glutamate oxaloacetate transaminase 1 (GOT1)

PDB DOI: https://doi.org/10.2210/pdb3II0/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-31 Released: 2009-08-11
Deposition Author(s): Ugochukwu, E., Pilka, E., Cooper, C., Bray, J.E., Yue, W.W., Muniz, J., Chaikuad, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.223
R-Value Work: 0.180
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of human Glutamate oxaloacetate transaminase 1 (GOT1)

Ugochukwu, E., Pilka, E., Cooper, C., Bray, J.E., Yue, W.W., Muniz, J., Chaikuad, A., Kavanagh, K.L., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 193.42 kDa
Atom Count: 13,751
Modelled Residue Count: 1,624
Deposited Residue Count: 1,688
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate aminotransferase, cytoplasmic	A, B, C, D	422	Homo sapiens	Mutation(s): 0 Gene Names: GOT1 EC: 2.6.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P17174 (Homo sapiens) Explore P17174 Go to UniProtKB: P17174
GTEx: ENSG00000120053
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17174
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth D]	E [auth A], J [auth B], O [auth C], U [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D]
TAR Query on TAR Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth D]	F [auth A], K [auth B], P [auth C], V [auth D]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain V [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	G [auth A] H [auth A] I [auth A] L [auth B] M [auth B] G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], W [auth D], X [auth D], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.223
R-Value Work: 0.180
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.531	α = 90
b = 107.347	β = 90
c = 239.997	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-08-11

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Advisory, Refinement description
Version 1.3: 2023-09-06
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description