9T4U | pdb_00009t4u

GDH in complex with ADP, processed with cryoPARES

PDB DOI: https://doi.org/10.2210/pdb9T4U/pdb
EM Map EMD-55532: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2025-10-31 Released: 2026-09-16
Deposition Author(s): Saur, M., Sachez-Garcia, R.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9T4U

This is version 1.0 of the entry. See complete history.

Literature

Supervised Deep Learning for Efficient Cryo-EM Image Alignment in Drug Discovery with cryoPARES

Sanchez-Garcia, R., Berndt, A., Apelbaum, A., Reeks, J., Williams, P.A., Poelking, C., Deane, C.M., Saur, M.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.03.04.641536

Macromolecule Content

Total Structure Weight: 331.85 kDa
Atom Count: 23,304
Modeled Residue Count: 2,958
Deposited Residue Count: 2,958
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase 1, mitochondrial	A B [auth C] C [auth B] D E A, B [auth C], C [auth B], D, E, F	493	Bos taurus	Mutation(s): 0 EC: 1.4.1.3
UniProt
Find proteins for P00366 (Bos taurus) Explore P00366 Go to UniProtKB: P00366
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00366
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth E] SDF format, chain J [auth D] SDF format, chain I [auth B] SDF format, chain H [auth C] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth C] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth C] mmCIF format, chain G [auth A]	G [auth A] H [auth C] I [auth B] J [auth D] K [auth E] G [auth A], H [auth C], I [auth B], J [auth D], K [auth E], L [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

Sachez-Garcia, R.

Funding Organization	Location	Grant Number
Other private		Astex Sustaining Innovation Post-doctoral Programme

Revision History (Full details and data files)

Version 1.0: 2026-09-16
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.