Research workbench
The crystal structure of CK2ALPHA in complex with compound 6
Analyse The crystal structure of CK2ALPHA in complex with compound 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ORK
- Type
- protein
- Length
- 647 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit alpha
- EC
- 2.7.11.1
- UniProt
- P68400
- Ligands
- ADP, A4T, MG, CL, PO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 323 | 40% helix, 16% strand | P68400 |
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 324 | 40% helix, 16% strand | P68400 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, A
- A4T · [3-chloranyl-4-(2-fluorophenyl)phenyl]methanamine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.76 | 0.84 | 56 | ADP, MG, A4T |
| 2 | 114 | 0.74 | 0.94 | 21 | empty |
| 3 | 411 | 0.69 | 0.80 | 37 | ADP |
| 4 | 461 | 0.63 | 0.77 | 48 | empty |
| 5 | 198 | 0.46 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- B–A · 565 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- P68400 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha (P68400) · a predicted model of the same protein · chain A 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 P68400
- Elsewhere: RCSB PDB 5ORK · PDBe 5ORK · UniProt P68400
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