Research workbench
Crystal structure of the dihydroxyacetone kinase from C. freundii in complex with AMP-pnp and MG2+
Analyse Crystal structure of the dihydroxyacetone kinase from C. freundii in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UN9
- Type
- protein
- Length
- 1,074 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroxyacetone kinase
- EC
- 2.7.1.29
- UniProt
- P45510
- Ligands
- ANP, 2HA, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroxyacetone kinase (EC 2.7.1.29) | protein | 537 | 45% helix, 16% strand | P45510 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- 2HA · Dihydroxyacetone · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.82 | 0.88 | 39 | empty |
| 2 | 1098 | 0.81 | 0.82 | 109 | empty |
| 3 | 471 | 0.80 | 0.86 | 40 | empty |
| 4 | 339 | 0.62 | 0.79 | 48 | empty |
| 5 | 220 | 0.51 | 0.76 | 33 | ANP |
Interfaces
1 interface between chains.
- A–B · 4930 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1UN9 · Crystal structure of the dihydroxyacetone kinase from C. freundii in complex with AMP-PNP… · the same entry in another collection · chain A against A, TM-score 1.00
- P45510 · AlphaFold monomer V2.0 prediction for dihydroxyacetone kinase (P45510) · a predicted model of the same protein · chain A against A, TM-score 0.71
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 P45510
- Elsewhere: RCSB PDB 1UN9 · PDBe 1UN9 · UniProt P45510
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