Research workbench
CK2 alpha bound to chemical probe SGC-CK2-1
Analyse CK2 alpha bound to chemical probe SGC-CK2-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z83
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.171
- Source
- Homo sapiens
- Molecule
- Casein kinase II subunit alpha
- EC
- 2.7.11.1
- UniProt
- P68400
- Ligands
- QBE, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.171 · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 327 | 43% helix, 16% strand | P68400 |
| BBB | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 330 | 44% helix, 15% strand | P68400 |
Ligands and binding sites
- QBE · ~{N}-[5-[[3-cyano-7-(cyclopropylamino)-3~{H}-pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]propanamide · ligand · 2 copies · chains AAA, BBB
- SO4 · Sulfate ion · ion · 12 copies · chains AAA, BBB
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains AAA, BBB
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.73 | 0.84 | 47 | PEG |
| 2 | 416 | 0.70 | 0.81 | 51 | SO4, QBE |
| 3 | 377 | 0.67 | 0.80 | 46 | SO4, QBE |
| 4 | 120 | 0.47 | 0.79 | 21 | empty |
| 5 | 110 | 0.41 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- AAA–BBB · 735 Ų buried · 13 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 AAA against A, TM-score 1.00
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 6Z83 · PDBe 6Z83 · UniProt P68400
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