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Crystal structure of a novel ADP-dependent glucokinase from thermococcus litoralis

Analyse Crystal structure of a novel ADP-dependent glucokinase from thermococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GC5
Type: protein
Length: 467 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-dependent glucokinase
EC: 2.7.1.147
UniProt: Q7M537
Ligands: ADP
Pockets: 3 · best druggability 0.74

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ADP-dependent glucokinase (EC 2.7.1.147)	protein	467	47% helix, 20% strand	Q7M537

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1055	0.74	0.77	72	ADP
2	177	0.66	0.86	30	empty
3	53	0.39	0.81	12	empty

Compared structures

1GC5 · Crystal structure of a novel ADP-dependent glucokinase from thermococcus litoralis · the same entry in another collection · chain A against A, TM-score 1.00
Q7M537 · AlphaFold monomer V2.0 prediction for ADP-dependent GLUCOSE/GLUCOSAMINE kinase (Q7M537) · a predicted model of the same protein · chain A 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 Q7M537
Elsewhere: RCSB PDB 1GC5 · PDBe 1GC5 · UniProt Q7M537

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