8KAO

Glutamate dehydrogenase-69O

• PDB DOI: https://doi.org/10.2210/pdb8KAO/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.260 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Structure of glutamate dehydrogenase-69O

Sakuraba, H., Ohshima, T.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 137.46 kDa 
• Atom Count: 9,341 
• Modelled Residue Count: 1,199 
• Deposited Residue Count: 1,257 
• Unique protein chains: 1

Macromolecules

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)) Go to UniProtKB:  Q97Y81

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	D [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
69O (Subject of Investigation/LOI)	E [auth C]	2-oxopentanoic acid C5 H8 O3 KDVFRMMRZOCFLS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.260 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.782	α = 90
b = 153.599	β = 115.58
c = 110.55	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Sakuraba, H., Ohshima, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release