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Crystal structure of aspergillus terreus glutamate dehydrogenase (atgdh) complexed with succinate and ADP-ribose

Analyse Crystal structure of aspergillus terreus glutamate dehydrogenase (atgdh)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ECR
Type: protein
Length: 1,380 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate dehydrogenase
UniProt: T2D1F5
Ligands: A2R
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Glutamate dehydrogenase	protein	460	48% helix, 16% strand	T2D1F5

Ligands and binding sites

A2R · [(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 3 copies · chains A, B, C
GOL · Glycerol · additive · 20 copies · chains A, B, C
SIN · Succinic acid · additive · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	757	0.78	0.82	82	SIN, A2R
2	727	0.78	0.83	74	SIN, A2R
3	709	0.78	0.83	71	GOL, SIN, A2R
4	551	0.73	0.81	62	empty
5	129	0.46	0.77	19	GOL

Interfaces

3 interfaces between chains.

A–C · 1016 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1012 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 993 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

7ECR · Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With… · the same entry in another collection · chain C against C, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt T2D1F5
Elsewhere: RCSB PDB 7ECR · PDBe 7ECR · UniProt T2D1F5

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