The crystal structure of CK2A bound to P2-C4

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).

Ligands and binding sites

• BEZ · Benzoic acid · ligand · 2 copies · chains A, B
• HEK · 3-[1-[(2~{S})-2-(2-acetamidoethanoylamino)-3-oxidanylidene-propyl]-1,2,3-triazol-4-yl]-5-[1-[(2~{S})-2-azanyl-3-[[2-[(2-azanyl-2-oxidanylidene-ethyl)amino]-2-oxidanylidene-ethyl]amino]-3-oxidanylidene-propyl]-1,2,3-triazol-4-yl]benzoic acid · ligand · 2 copies · chains C, B, D
• GOL · Glycerol · additive · 3 copies · chains A, B
• ACT · Acetate ion · additive · 2 copies · chains A, B

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.

Interfaces

3 interfaces between chains.

• A–B · 610 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 606 Ų buried · 7 hydrogen bonds · protein-protein
• B–D · 604 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 6Q4Q · The Crystal structure of CK2a bound to P2-C4 · the same entry in another collection · chain A against A, TM-score 1.00
• 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 6Q4Q · PDBe 6Q4Q · UniProt P68400