Research workbench
Ternary complex of human pancreatic glucokinase crystallized with activator, glucose and AMP-pnp
Analyse Ternary complex of human pancreatic glucokinase crystallized with activator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ID8
- Type
- protein
- Length
- 450 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase
- EC
- 2.7.1.2
- UniProt
- P35557
- Ligands
- MRK, ANP, GLC, MG, K
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucokinase (EC 2.7.1.2) | protein | 450 | 46% helix, 21% strand | P35557 |
Ligands and binding sites
- MRK · 2-amino-4-fluoro-5-[(1-methyl-1H-imidazol-2-yl)sulfanyl]-N-(1,3-thiazol-2-yl)benzamide · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- MG · Magnesium ion · metal · chains A
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.63 | 0.81 | 38 | GLC, ANP, MG |
| 2 | 188 | 0.59 | 0.81 | 24 | MRK |
| 3 | 101 | 0.36 | 0.74 | 23 | ANP |
| 4 | 60 | 0.35 | 0.78 | 16 | empty |
| 5 | 67 | 0.33 | 0.76 | 13 | empty |
Compared structures
- 3ID8 · Ternary complex of human pancreatic glucokinase crystallized with activator, glucose and… · the same entry in another collection · chain A against A, TM-score 1.00
- P35557 · AlphaFold monomer V2.0 prediction for hexokinase-4 (P35557) · 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 P35557
- Elsewhere: RCSB PDB 3ID8 · PDBe 3ID8 · UniProt P35557
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