Research workbench
Crystal structure of human choline kinase beta in complex with phosphorylated hemicholinium-3 and adenosine nucleotide
Analyse Crystal structure of human choline kinase beta in complex with phosphorylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LQ3
- Type
- protein
- Length
- 339 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CHOLINE/ETHANOLAMINE kinase
- EC
- 2.7.1.32, 2.7.1.82
- UniProt
- Q9Y259
- Ligands
- HC7, ADP, AMP, MG, UNX, SO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CHOLINE/ETHANOLAMINE kinase (EC 2.7.1.32, 2.7.1.82) | protein | 339 | 51% helix, 13% strand | Q9Y259 |
Ligands and binding sites
- HC7 · (2S)-2-[4'-({dimethyl[2-(phosphonooxy)ethyl]ammonio}acetyl)biphenyl-4-yl]-2-hydroxy-4,4-dimethylmorpholin-4-ium · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- UNX · Unknown atom or ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.68 | 0.76 | 69 | HC7, MG, UNX, ADP, AMP |
| 2 | 148 | 0.48 | 0.78 | 15 | empty |
| 3 | 81 | 0.37 | 0.76 | 15 | empty |
Compared structures
- 3LQ3 · Crystal structure of human choline kinase beta in complex with phosphorylated… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y259 · AlphaFold monomer V2.0 prediction for CHOLINE/ETHANOLAMINE kinase (Q9Y259) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9Y259
- Elsewhere: RCSB PDB 3LQ3 · PDBe 3LQ3 · UniProt Q9Y259
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