MolNFT v1 · #160211 · protein

Cryoem structure of yeast glucokinase filament

6PDT · Glucokinase-1: “Cryoem structure of yeast glucokinase filament”. Electron microscopy, 3 ligands (ATP, GLC, MG), 20 pockets (best druggability 0.85). MolNFT v1 #160211 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PDT
Type: protein
Length: 2,000 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucokinase-1
EC: 2.7.1.2
UniProt: P17709
Ligands: ATP, GLC, MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glucokinase-1 (EC 2.7.1.2)	protein	500	46% helix, 18% strand	P17709

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1158	0.85	0.86	143	GLC, MG, ATP
2	760	0.77	0.81	93	empty
3	267	0.76	0.90	52	GLC, MG, ATP
4	232	0.76	0.90	47	GLC, MG, ATP
5	130	0.64	0.87	30	empty

Interfaces

5 interfaces between chains.

C–D · 1401 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1375 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 769 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 763 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 567 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6PDT · cryoEM structure of yeast glucokinase filament · the same entry in another collection · chain A against A, 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 0.98

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 6PDT · PDBe 6PDT · UniProt P17709

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