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Crystal structure of glutamate 5-kinase from campylobacter jejuni

Analyse Crystal structure of glutamate 5-kinase from campylobacter jejuni in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2AKO
Type: protein
Length: 964 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate 5-kinase
EC: 2.7.2.11
UniProt: Q9PJ29
Ligands: ADP
Pockets: 13 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glutamate 5-kinase (EC 2.7.2.11)	protein	241	47% helix, 20% strand	Q9PJ29

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	480	0.68	0.79	54	empty
2	504	0.67	0.78	60	empty
3	183	0.58	0.81	25	empty
4	187	0.58	0.81	24	empty
5	217	0.56	0.79	38	empty

Interfaces

6 interfaces between chains.

A–B · 1503 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1443 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 304 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 282 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 89 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

2AKO · Crystal structure of Glutamate 5-kinase from Campylobacter jejuni · the same entry in another collection · chain A against A, TM-score 1.00
Q9PJ29 · AlphaFold monomer V2.0 prediction for glutamate 5-kinase (Q9PJ29) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9PJ29
Elsewhere: RCSB PDB 2AKO · PDBe 2AKO · UniProt Q9PJ29

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