MolNFT v1 · #60961 · protein
Enterococcus casseliflavus glycerol kinase mutant HIS232ALA complexed with glycerol
3D7E: “Enterococcus casseliflavus glycerol kinase mutant HIS232ALA complexed with glycerol”. X-ray diffraction, 7 pockets (best druggability 0.73). MolNFT v1 #60961 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3D7E
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- O34153
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, X | Glycerol kinase (EC 2.7.1.30) | protein | 495 | 37% helix, 25% strand | O34153 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains O, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.73 | 0.82 | 63 | GOL |
| 2 | 439 | 0.71 | 0.82 | 51 | GOL |
| 3 | 343 | 0.64 | 0.80 | 52 | empty |
| 4 | 258 | 0.59 | 0.79 | 48 | empty |
| 5 | 102 | 0.57 | 0.85 | 22 | empty |
Interfaces
1 interface between chains.
- O–X · 1819 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3D7E · Enterococcus casseliflavus glycerol kinase mutant HIS232ALA complexed with glycerol · the same entry in another collection · chain O against O, TM-score 1.00
- O34153 · AlphaFold monomer V2.0 prediction for glycerol kinase (O34153) · a predicted model of the same protein · chain O against A, TM-score 0.99
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 O34153
- Elsewhere: RCSB PDB 3D7E · PDBe 3D7E · UniProt O34153
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