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Crystal structure of the S. cerevisiae glucokinase, GLK1

Analyse Crystal structure of the S. cerevisiae glucokinase, GLK1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P4X
Type: protein
Length: 2,944 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucokinase-1
EC: 2.7.1.2
UniProt: P17709
Ligands: PO4
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucokinase-1 (EC 2.7.1.2)	protein	491	41% helix, 17% strand	P17709
B	Glucokinase-1 (EC 2.7.1.2)	protein	490	42% helix, 16% strand	P17709
C, F	Glucokinase-1 (EC 2.7.1.2)	protein	493	42% helix, 15% strand	P17709
D	Glucokinase-1 (EC 2.7.1.2)	protein	488	41% helix, 16% strand	P17709
E	Glucokinase-1 (EC 2.7.1.2)	protein	489	44% helix, 15% strand	P17709

Ligands and binding sites

PO4 · Phosphate ion · ion · 13 copies · chains A, C, B, E, D, F

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	225	0.72	0.87	33	empty
2	157	0.70	0.89	32	empty
3	702	0.67	0.75	77	PO4
4	432	0.67	0.79	56	empty
5	518	0.67	0.78	65	empty

Interfaces

6 interfaces between chains.

B–E · 1757 Å² buried · 27 hydrogen bonds · protein-protein
D–F · 1719 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 1678 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 1520 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1484 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6P4X · Crystal Structure of the S. cerevisiae glucokinase, Glk1 · the same entry in another collection · chain F against F, TM-score 1.00
P17709 · AlphaFold monomer V2.0 prediction for glucokinase-1 (P17709) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P17709
Elsewhere: RCSB PDB 6P4X · PDBe 6P4X · UniProt P17709

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