MolNFT v1 · #17089 · protein
X-ray structure of the dihydroxyacetone kinase from escherichia COLI
1OI3 · Hypothetical protein ycgt: “X-ray structure of the dihydroxyacetone kinase from escherichia COLI”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.81). MolNFT v1 #17089 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1OI3
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein ycgt
- EC
- 2.7.1.29
- UniProt
- P76015
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein ycgt (EC 2.7.1.29) | protein | 336 | 32% helix, 31% strand | P76015 |
Ligands and binding sites
- 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.81 | 0.82 | 94 | SO4 |
| 2 | 59 | 0.68 | 0.96 | 24 | empty |
| 3 | 52 | 0.32 | 0.77 | 16 | empty |
| 4 | 54 | 0.32 | 0.77 | 18 | empty |
| 5 | 62 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1305 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1OI3 · X-ray structure of the dihydroxyacetone kinase from Escherichia coli · 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 1OI3 · PDBe 1OI3 · UniProt P76015
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