Minimal construct of CDC7-DBF4 bound to XL413

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 17% strand (DSSP).

Ligands and binding sites

• 0SX · 8-chloro-2-[(2S)-pyrrolidin-2-yl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one · ligand · chains A
• ZN · Zinc ion · metal · 2 copies · chains A, B
• BO3 · Boric acid · ion · chains A
• CL · Chloride ion · ion · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · chains A
• IMD · Imidazole · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3650 Ų buried · 51 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

• 6YA6 · Minimal construct of Cdc7-Dbf4 bound to XL413 · the same entry in another collection · chain A against A, TM-score 1.00
• O00311 · AlphaFold monomer V2.0 prediction for cell division cycle 7-related protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.99
• Q9UBU7 · AlphaFold monomer V2.0 prediction for protein DBF4 homolog a (Q9UBU7) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 O00311
• Every structure of UniProt Q9UBU7
• Elsewhere: RCSB PDB 6YA6 · PDBe 6YA6 · UniProt O00311 · UniProt Q9UBU7