8KAR

Glutamate dehydrogenase-AKG

PDB DOI: https://doi.org/10.2210/pdb8KAR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-03 Released: 2024-08-07
Deposition Author(s): Sakuraba, H., Ohshima, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.231
R-Value Work: 0.197
R-Value Observed: 0.198

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of glutamate dehydrogenase-AKG

Sakuraba, H., Ohshima, T.

To be published.

Macromolecule Content

Total Structure Weight: 139.92 kDa
Atom Count: 10,112
Modelled Residue Count: 1,242
Deposited Residue Count: 1,257
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C	419	Saccharolobus solfataricus	Mutation(s): 0 Gene Names: HFC64_02080
UniProt
Find proteins for Q97Y81 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97Y81 Go to UniProtKB: Q97Y81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q97Y81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C]	E [auth A], L [auth B], R [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C]
AKG (Subject of Investigation/LOI) Query on AKG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C]	D [auth A], K [auth B], Q [auth C]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain Q [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]