9YB6 | pdb_00009yb6

Human Mitochondrial Aspartate Aminotransferase complex with PLP at 1.5 Angstrom.

PDB DOI: https://doi.org/10.2210/pdb9YB6/pdb

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

Deposited: 2025-09-16 Released: 2025-09-24
Deposition Author(s): Krinkel, B.A., Yosaatmadja, Y., Squire, C.J., Loomes, K.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.209 (Depositor), 0.211 (DCC)
R-Value Work:
0.185 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Human mitochondrial GOT2 crystal structure and...

Krinkel, B.A., Yosaatmadja, Y., Squire, C.J., Loomes, K.M.

To be published.

Macromolecule Content

Total Structure Weight: 96.46 kDa
Atom Count: 7,496
Modeled Residue Count: 805
Deposited Residue Count: 860
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate aminotransferase, mitochondrial	A, B	430	Homo sapiens	Mutation(s): 0 Gene Names: GOT2, KYAT4 EC: 2.6.1.1 (PDB Primary Data), 2.6.1.7 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P00505 (Homo sapiens) Explore P00505 Go to UniProtKB: P00505
PHAROS: P00505 GTEx: ENSG00000125166
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00505
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.209 (Depositor), 0.211 (DCC)
R-Value Work: 0.185 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.18	α = 101.393
b = 59.168	β = 101.722
c = 67.167	γ = 95.408

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Yosaatmadja, Y.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-09-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.