Research workbench
Insights into glucokinase activation mechanism: observation of multiple distinct protein conformations
Analyse Insights into glucokinase activation mechanism: observation of multiple… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DCH
- Type
- protein
- Length
- 434 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
- 4DC, GLC, IOD
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucokinase (EC 2.7.1.2) | protein | 434 | 48% helix, 18% strand | P35557 |
Ligands and binding sites
- 4DC · (2R)-3-cyclopentyl-2-[4-(methylsulfonyl)phenyl]-N-(1,3-thiazol-2-yl)propanamide · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- IOD · Iodide ion · ion · 2 copies · 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 | 287 | 0.68 | 0.83 | 36 | 4DC |
| 2 | 271 | 0.60 | 0.80 | 33 | empty |
| 3 | 65 | 0.32 | 0.75 | 12 | empty |
| 4 | 64 | 0.31 | 0.75 | 18 | empty |
| 5 | 59 | 0.28 | 0.74 | 18 | empty |
Compared structures
- 4DCH · Insights into Glucokinase Activation Mechanism: Observation of Multiple Distinct Protein… · 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 0.83
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 4DCH · PDBe 4DCH · UniProt P35557
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