MolNFT v1 · #52544 · protein
Crystal structure of plasmodium falciparum glycerol kinase with ADP
2W41 · Glycerol kinase, putative: “Crystal structure of plasmodium falciparum glycerol kinase with ADP”. X-ray diffraction, 1 ligand (ADP), 12 pockets (best druggability 0.71). MolNFT v1 #52544 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2W41
- Type
- protein
- Length
- 1,013 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase, putative
- EC
- 2.7.1.30
- UniProt
- Q8IDI4
- Ligands
- ADP
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol kinase, putative (EC 2.7.1.30) | protein | 506 | 37% helix, 25% strand | Q8IDI4 |
| B | Glycerol kinase, putative (EC 2.7.1.30) | protein | 507 | 38% helix, 24% strand | Q8IDI4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.71 | 0.77 | 67 | EDO |
| 2 | 725 | 0.71 | 0.78 | 60 | EDO |
| 3 | 199 | 0.56 | 0.79 | 32 | empty |
| 4 | 200 | 0.53 | 0.78 | 32 | EDO |
| 5 | 111 | 0.39 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1467 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2W41 · Crystal structure of Plasmodium falciparum glycerol kinase with ADP · 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 2W41 · PDBe 2W41 · UniProt Q8IDI4
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