Research workbench
Crystal structure of human choline kinase alpha-2 in complex with ADP
Analyse Crystal structure of human choline kinase alpha-2 in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CKP
- Type
- protein
- Length
- 590 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
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline kinase alpha (EC 2.7.1.32) | protein | 316 | 54% helix, 13% strand | P35790 |
| B | Choline kinase alpha (EC 2.7.1.32) | protein | 274 | 43% helix, 15% strand | P35790 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.71 | 0.76 | 60 | ADP |
| 2 | 213 | 0.52 | 0.77 | 36 | empty |
| 3 | 167 | 0.50 | 0.77 | 23 | empty |
| 4 | 104 | 0.49 | 0.81 | 27 | empty |
| 5 | 140 | 0.45 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2CKP · Crystal structure of Human Choline Kinase alpha-2 in complex with 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 A against A, TM-score 0.97
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 2CKP · PDBe 2CKP · UniProt P35790
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