Research workbench
Crystal structure of glucokinase with bound glucose from acanthamoeba castellanii
Analyse Crystal structure of glucokinase with bound glucose from acanthamoeba… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DTC
- Type
- protein
- Length
- 748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase
- UniProt
- L8GT25
- Ligands
- BGC, SO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucokinase | protein | 374 | 43% helix, 20% strand | L8GT25 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.73 | 0.99 | 17 | empty |
| 2 | 472 | 0.73 | 0.83 | 62 | BGC |
| 3 | 488 | 0.72 | 0.82 | 58 | BGC |
| 4 | 348 | 0.68 | 0.82 | 51 | EDO |
| 5 | 308 | 0.67 | 0.82 | 40 | EDO |
Interfaces
1 interface between chains.
- A–B · 2467 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 8DTC · Crystal Structure of Glucokinase with bound glucose from Acanthamoeba castellanii · the same entry in another collection · chain A against A, TM-score 1.00
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 L8GT25
- Elsewhere: RCSB PDB 8DTC · PDBe 8DTC · UniProt L8GT25
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