MolNFT v1 · #153303 · protein
Crystal structure of trypanosoma brucei gambiense glycerol kinase complex with pi (pyrophosphatase reaction)
6JAE: “Crystal structure of trypanosoma brucei gambiense glycerol kinase complex with pi (pyrophosphatase reaction)”. X-ray diffraction, 1 ligand (PO4), 14 pockets (best druggability 0.74). MolNFT v1 #153303 on GenesisL1: 3D structure…
- PDB
- 6JAE
- 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
- PO4
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycerol kinase (EC 2.7.1.30) | protein | 513 | 37% helix, 25% strand | D3KVM3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
- 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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.74 | 0.77 | 83 | PO4, GOL |
| 2 | 879 | 0.74 | 0.78 | 80 | PO4, GOL |
| 3 | 744 | 0.70 | 0.77 | 65 | GOL |
| 4 | 668 | 0.69 | 0.77 | 74 | GOL |
| 5 | 293 | 0.58 | 0.77 | 29 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1385 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1385 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 536 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6JAE · Crystal structure of Trypanosoma brucei gambiense glycerol kinase complex with Pi… · 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 6JAE · PDBe 6JAE · UniProt D3KVM3
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