Research workbench
Crystal structure of glycerol kinase from trypanosoma brucei gambiense complexed with cumarin derivative-17B
Analyse Crystal structure of glycerol kinase from trypanosoma brucei gambiense… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GN6
- 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
- Ligands
- 6Y0
- Pockets
- 16 · 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
- 6Y0 · 4-butyl-7,8-bis(oxidanyl)chromen-2-one · ligand · 4 copies · chains A, B, C, D
- 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
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.75 | 0.79 | 68 | 6Y0, GOL |
| 2 | 865 | 0.72 | 0.77 | 77 | 6Y0, GOL |
| 3 | 666 | 0.70 | 0.78 | 62 | 6Y0, GOL |
| 4 | 93 | 0.70 | 0.93 | 19 | empty |
| 5 | 741 | 0.70 | 0.77 | 66 | 6Y0, GOL |
Interfaces
3 interfaces between chains.
- A–B · 1399 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1384 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5GN6 · Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with… · 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 5GN6 · PDBe 5GN6 · UniProt D3KVM3
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