Research workbench
Crystal structure of glycerol kinase from trypanosoma brucei gambiense complexed with 4NP (with disulfide bridge)
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
- 5AZJ
- 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
- 4NP
- Pockets
- 15 · best druggability 0.70
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
- 4NP · 4-nitrophenyl phosphate · ligand · 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
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.70 | 0.77 | 77 | 4NP, GOL |
| 2 | 617 | 0.69 | 0.78 | 56 | 4NP, GOL |
| 3 | 591 | 0.69 | 0.78 | 53 | empty |
| 4 | 541 | 0.68 | 0.78 | 55 | empty |
| 5 | 77 | 0.67 | 0.93 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1392 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1381 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 426 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, phosphorylation).
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 5AZJ · PDBe 5AZJ · UniProt D3KVM3
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