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Crystal structure of trypanosoma brucei gambiense glycerol kinase in complex with glycerol
Analyse Crystal structure of trypanosoma brucei gambiense glycerol kinase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WXK
- Type
- protein
- Length
- 2,052 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- D3KVM3
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycerol kinase (EC 2.7.1.30) | protein | 513 | 37% helix, 24% strand | D3KVM3 |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- HEZ · Hexane-1,6-diol · additive · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.75 | 0.78 | 79 | GOL, HEZ |
| 2 | 834 | 0.72 | 0.77 | 79 | GOL, HEZ |
| 3 | 747 | 0.71 | 0.77 | 67 | GOL |
| 4 | 701 | 0.69 | 0.77 | 61 | GOL |
| 5 | 333 | 0.60 | 0.77 | 36 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1430 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1373 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 473 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3WXK · Crystal structure of trypanosoma brucei gambiense glycerol kinase in complex with 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 D3KVM3
- Elsewhere: RCSB PDB 3WXK · PDBe 3WXK · UniProt D3KVM3
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