MolNFT v1 · #24228 · protein
Crystal structure of the dihydroxyacetone kinase from E. COLI in complex with dihydroxyacetone-phosphate
1UOD: “Crystal structure of the dihydroxyacetone kinase from E. COLI in complex with dihydroxyacetone-phosphate”. X-ray diffraction, 2 ligands (G3H, SO4), 6 pockets (best druggability 0.82). MolNFT v1 #24228 on GenesisL1: 3D structure…
- PDB
- 1UOD
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroxyacetone kinase
- EC
- 2.7.1.29
- UniProt
- P76015
- Ligands
- G3H, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroxyacetone kinase (EC 2.7.1.29) | protein | 336 | 32% helix, 32% strand | P76015 |
Ligands and binding sites
- G3H · Glyceraldehyde-3-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.82 | 0.83 | 116 | SO4 |
| 2 | 66 | 0.40 | 0.80 | 16 | empty |
| 3 | 82 | 0.39 | 0.77 | 26 | empty |
| 4 | 57 | 0.37 | 0.80 | 16 | empty |
| 5 | 66 | 0.33 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1290 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1UOD · Crystal structure of the dihydroxyacetone kinase from E. coli in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P76015 · AlphaFold monomer V2.0 prediction for pep-dependent dihydroxyacetone kinase… · a predicted model of the same protein · 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 P76015
- Elsewhere: RCSB PDB 1UOD · PDBe 1UOD · UniProt P76015
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