Research workbench

E. COLI 2-oxoglutarate dehydrogenase (E1o)

Analyse E. COLI 2-oxoglutarate dehydrogenase (E1o) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2JGD
Type: protein
Length: 1,619 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.6
Source: ESCHERICHIA COLI
Molecule: 2-oxoglutarate dehydrogenase E1 component
EC: 1.2.4.2
UniProt: P0AFG3
Ligands: AMP
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · resolution 2.6 · 2 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-oxoglutarate dehydrogenase E1 component (EC 1.2.4.2)	protein	812	43% helix, 15% strand	P0AFG3
B	2-oxoglutarate dehydrogenase E1 component (EC 1.2.4.2)	protein	807	45% helix, 15% strand	P0AFG3

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	953	0.82	0.84	132	empty
2	927	0.74	0.78	84	empty
3	50	0.70	0.98	26	empty
4	50	0.69	0.98	17	empty
5	472	0.63	0.76	55	AMP

Interfaces

1 interface between chains.

A–B · 2907 Å² buried · 44 hydrogen bonds · protein-protein

Compared structures

2JGD · E. COLI 2-oxoglutarate dehydrogenase (E1O) · the same entry in another collection · chain A against A, TM-score 1.00
P0AFG3 · AlphaFold monomer V2.0 prediction for 2-oxoglutarate dehydrogenase E1 component (P0AFG3) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P0AFG3
Elsewhere: RCSB PDB 2JGD · PDBe 2JGD · UniProt P0AFG3

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