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Crystal structure of Trypanosoma brucei gambiense glycerol kinase phosphorylated at Thr12(pyrophosphatase reaction)
Analyse Crystal structure of Trypanosoma brucei gambiense glycerol kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J9X
- Type
- protein
- Length
- 2,052 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Trypanosoma brucei gambiense
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- D3KVM3
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.7 · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycerol kinase (EC 2.7.1.30) | protein | 513 | 34% helix, 22% strand | D3KVM3 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.75 | 0.78 | 90 | GOL |
| 2 | 827 | 0.74 | 0.79 | 79 | GOL |
| 3 | 792 | 0.74 | 0.79 | 66 | GOL |
| 4 | 794 | 0.73 | 0.78 | 62 | GOL |
| 5 | 352 | 0.60 | 0.77 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1394 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1385 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 454 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6J9X · Crystal structure of trypanosoma brucei gambiense glycerol kinase phosphorylated at… · 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 6J9X · PDBe 6J9X · UniProt D3KVM3
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