Research workbench
Crystal structure of glucokinase from enterococcus faecalis
Analyse Crystal structure of glucokinase from enterococcus faecalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QM1
- Type
- protein
- Length
- 1,297 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase
- UniProt
- Q830J4
- Ligands
- MG, ZN, SO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glucokinase | protein | 324 | 44% helix, 23% strand | Q830J4 |
| B | Glucokinase | protein | 325 | 45% helix, 22% strand | Q830J4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains D
- GOL · Glycerol · additive · 6 copies · chains A, C, B
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.74 | 0.77 | 94 | empty |
| 2 | 698 | 0.70 | 0.78 | 66 | empty |
| 3 | 95 | 0.62 | 0.88 | 27 | empty |
| 4 | 484 | 0.60 | 0.75 | 55 | empty |
| 5 | 110 | 0.60 | 0.86 | 29 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1595 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1522 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 387 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 343 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2QM1 · Crystal structure of glucokinase from Enterococcus faecalis · 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 Q830J4
- Elsewhere: RCSB PDB 2QM1 · PDBe 2QM1 · UniProt Q830J4
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