MolNFT v1 · #65667 · protein
Glycerol kinase H232R with glycerol
3H3N: “Glycerol kinase H232R with glycerol”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.72). MolNFT v1 #65667 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3H3N
- Type
- protein
- Length
- 1,002 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
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, O | Glycerol kinase (EC 2.7.1.30) | protein | 501 | 37% helix, 24% strand | O34153 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains X, O
- EDO · 1,2-ethanediol · additive · 6 copies · chains X, O
- GOL · Glycerol · additive · 2 copies · chains X, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.72 | 0.81 | 53 | GOL, EDO, PO4 |
| 2 | 518 | 0.71 | 0.80 | 49 | GOL, PO4 |
| 3 | 206 | 0.66 | 0.84 | 26 | EDO |
| 4 | 139 | 0.59 | 0.84 | 24 | empty |
| 5 | 179 | 0.54 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- X–O · 470 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 3H3N · PDBe 3H3N · UniProt O34153
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