MolNFT v1 · #52543 · protein
Crystal structure of plasmodium falciparum glycerol kinase with bound glycerol
2W40 · Glycerol kinase, putative: “Crystal structure of plasmodium falciparum glycerol kinase with bound glycerol”. X-ray diffraction, 20 pockets (best druggability 0.68). MolNFT v1 #52543 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2W40
- Type
- protein
- Length
- 2,009 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase, putative
- EC
- 2.7.1.30
- UniProt
- Q8IDI4
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol kinase, putative (EC 2.7.1.30) | protein | 501 | 39% helix, 24% strand | Q8IDI4 |
| B, D | Glycerol kinase, putative (EC 2.7.1.30) | protein | 503 | 38% helix, 24% strand | Q8IDI4 |
| C | Glycerol kinase, putative (EC 2.7.1.30) | protein | 502 | 38% helix, 24% strand | Q8IDI4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 62 copies · chains A, C, B, D
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.68 | 0.78 | 72 | empty |
| 2 | 357 | 0.64 | 0.79 | 45 | EDO, GOL |
| 3 | 330 | 0.63 | 0.79 | 45 | GOL |
| 4 | 309 | 0.63 | 0.80 | 41 | GOL |
| 5 | 328 | 0.63 | 0.79 | 48 | EDO, GOL |
Interfaces
4 interfaces between chains.
- B–D · 1773 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1768 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 235 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 202 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2W40 · Crystal structure of Plasmodium falciparum glycerol kinase with bound glycerol · 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 Q8IDI4
- Elsewhere: RCSB PDB 2W40 · PDBe 2W40 · UniProt Q8IDI4
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