Macromolecule Content

Total Structure Weight: 340.12 kDa
Atom Count: 24160
Residue Count: 2960
Unique protein chains: 1

6G2U

Crystal structure of the human glutamate dehydrogenase 2 (hGDH2)

DOI: 10.2210/pdb6G2U/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2018-03-23 Released: 2019-04-10
Deposition Author(s): Fadouloglou, V.F., Dimovasili, C., Providaki, M., Kotsifaki, D., Sarrou, I., Plaitakis, A., Zaganas, I., Kokkinidis, M.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.93 Å
R-Value Free: 0.249
R-Value Work: 0.193
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the human glutamate dehydrogenase 2 (hGDH2)

Fadouloglou, V.F., Dimovasili, C., Providaki, M., Kotsifaki, D., Sarrou, I., Plaitakis, A., Zaganas, I., Kokkinidis, M.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase 2, mitochondrial	A, B, C, D, E, F	505	Homo sapiens	Mutation(s): 0 Gene Names: GLUD2, GLUDP1 EC: 1.4.1.3
Find proteins for P49448 (Homo sapiens) Explore P49448 Go to UniProtKB: P49448
NIH Common Fund Data Resources
PHAROS P49448 GTEx ENSG00000182890
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [C] SDF format, chain FA [D] SDF format, chain G [A] SDF format, chain GA [D] SDF format, chain H [A] SDF format, chain I [A] SDF format, chain IB [F] SDF format, chain J [A] SDF format, chain JB [F] SDF format, chain KB [F] SDF format, chain LB [F] SDF format, chain MB [F] SDF format, chain P [B] SDF format, chain Q [B] SDF format, chain R [B] SDF format, chain S [B] SDF format, chain T [B] SDF format, chain W [C] SDF format, chain X [C] SDF format, chain XA [E] SDF format, chain Y [C] SDF format, chain YA [E] SDF format, chain Z [C] MOL2 format, chain AA [C] MOL2 format, chain FA [D] MOL2 format, chain G [A] MOL2 format, chain GA [D] MOL2 format, chain H [A] MOL2 format, chain I [A] MOL2 format, chain IB [F] MOL2 format, chain J [A] MOL2 format, chain JB [F] MOL2 format, chain KB [F] MOL2 format, chain LB [F] MOL2 format, chain MB [F] MOL2 format, chain P [B] MOL2 format, chain Q [B] MOL2 format, chain R [B] MOL2 format, chain S [B] MOL2 format, chain T [B] MOL2 format, chain W [C] MOL2 format, chain X [C] MOL2 format, chain XA [E] MOL2 format, chain Y [C] MOL2 format, chain YA [E] MOL2 format, chain Z [C]	A, B, C, D, E, F	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CB [E] SDF format, chain DA [C] SDF format, chain DB [E] SDF format, chain EA [C] SDF format, chain EB [E] SDF format, chain FB [E] SDF format, chain GB [E] SDF format, chain HB [E] SDF format, chain M [A] SDF format, chain N [A] SDF format, chain O [A] SDF format, chain QB [F] SDF format, chain SA [D] SDF format, chain TA [D] SDF format, chain U [B] SDF format, chain UA [D] SDF format, chain V [B] SDF format, chain VA [D] SDF format, chain WA [D] MOL2 format, chain CB [E] MOL2 format, chain DA [C] MOL2 format, chain DB [E] MOL2 format, chain EA [C] MOL2 format, chain EB [E] MOL2 format, chain FB [E] MOL2 format, chain GB [E] MOL2 format, chain HB [E] MOL2 format, chain M [A] MOL2 format, chain N [A] MOL2 format, chain O [A] MOL2 format, chain QB [F] MOL2 format, chain SA [D] MOL2 format, chain TA [D] MOL2 format, chain U [B] MOL2 format, chain UA [D] MOL2 format, chain V [B] MOL2 format, chain VA [D] MOL2 format, chain WA [D]	A, B, C, D, E, F	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [E] SDF format, chain BA [C] SDF format, chain BB [E] SDF format, chain CA [C] SDF format, chain HA [D] SDF format, chain IA [D] SDF format, chain JA [D] SDF format, chain K [A] SDF format, chain KA [D] SDF format, chain L [A] SDF format, chain LA [D] SDF format, chain MA [D] SDF format, chain NA [D] SDF format, chain NB [F] SDF format, chain OA [D] SDF format, chain OB [F] SDF format, chain PA [D] SDF format, chain PB [F] SDF format, chain QA [D] SDF format, chain RA [D] SDF format, chain ZA [E] MOL2 format, chain AB [E] MOL2 format, chain BA [C] MOL2 format, chain BB [E] MOL2 format, chain CA [C] MOL2 format, chain HA [D] MOL2 format, chain IA [D] MOL2 format, chain JA [D] MOL2 format, chain K [A] MOL2 format, chain KA [D] MOL2 format, chain L [A] MOL2 format, chain LA [D] MOL2 format, chain MA [D] MOL2 format, chain NA [D] MOL2 format, chain NB [F] MOL2 format, chain OA [D] MOL2 format, chain OB [F] MOL2 format, chain PA [D] MOL2 format, chain PB [F] MOL2 format, chain QA [D] MOL2 format, chain RA [D] MOL2 format, chain ZA [E]	A, C, D, E, F	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.93 Å
R-Value Free: 0.249
R-Value Work: 0.193
R-Value Observed: 0.196
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.795	α = 90
b = 149.304	β = 90
c = 433.315	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2018-03-23
Released Date: 2019-04-10

Deposition Author(s):

Fadouloglou, V.F.

Funding Organization	Location	Grant Number
European Commission	Greece	316223

Revision History

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2019-11-06
Changes: Data collection, Refinement description

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.