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Crystal structure of human choline kinase alpha in complex with hemicholinium-3 and ADP
Analyse Crystal structure of human choline kinase alpha in complex with hemicholinium-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G15
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline kinase alpha
- EC
- 2.7.1.32
- UniProt
- P35790
- Ligands
- ADP, HC6, MG, UNX, SO4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline kinase alpha (EC 2.7.1.32) | protein | 354 | 54% helix, 15% strand | P35790 |
| B | Choline kinase alpha (EC 2.7.1.32) | protein | 306 | 55% helix, 12% strand | P35790 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- HC6 · (2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorpholin-4-ium) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- UNX · Unknown atom or ion · ion · 21 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.68 | 0.77 | 58 | ADP, MG, HC6, SO4 |
| 2 | 293 | 0.55 | 0.76 | 37 | empty |
| 3 | 192 | 0.51 | 0.77 | 31 | UNX |
| 4 | 148 | 0.48 | 0.78 | 23 | MG, HC6, SO4 |
| 5 | 106 | 0.43 | 0.77 | 21 | ADP |
Interfaces
1 interface between chains.
- A–B · 1073 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3G15 · Crystal structure of human choline kinase alpha in complex with hemicholinium-3 and ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P35790 · AlphaFold monomer V2.0 prediction for choline kinase alpha (P35790) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P35790
- Elsewhere: RCSB PDB 3G15 · PDBe 3G15 · UniProt P35790
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