MolNFT v1 · #34094 · protein
Crystal structure of glycerol kinase from cellulomonas sp. NT3060
2D4W: “Crystal structure of glycerol kinase from cellulomonas sp. NT3060”. X-ray diffraction, 7 pockets (best druggability 0.69). MolNFT v1 #34094 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2D4W
- Type
- protein
- Length
- 1,006 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycerol kinase (EC 2.7.1.30) | protein | 503 | 37% helix, 23% strand | — |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.69 | 0.77 | 58 | MPD |
| 2 | 639 | 0.68 | 0.77 | 56 | MPD |
| 3 | 112 | 0.56 | 0.83 | 20 | MPD |
| 4 | 95 | 0.56 | 0.85 | 15 | MPD |
| 5 | 67 | 0.39 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1621 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2D4W · Crystal structure of glycerol kinase from Cellulomonas sp. NT3060 · 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
- Elsewhere: RCSB PDB 2D4W · PDBe 2D4W
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