CDC7-DBF4 bound to an MCM2-S40 derived bivalent substrate

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 17% strand (DSSP).

Ligands and binding sites

• ADP · Adenosine-5'-diphosphate · ligand · chains A, C
• ZN · Zinc ion · metal · 4 copies · chains A, C, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 3746 Ų buried · 47 hydrogen bonds · protein-protein
• A–C · 808 Ų buried · 14 hydrogen bonds · protein-protein
• B–C · 110 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard, phosphorylation).

Compared structures

• 6YA7 · Cdc7-Dbf4 bound to an Mcm2-S40 derived bivalent substrate · 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 0.98
• 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
• P49736 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM2 (P49736) · a predicted model of the same protein · chain C against A, TM-score 0.53

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
• Every structure of UniProt P49736
• Elsewhere: RCSB PDB 6YA7 · PDBe 6YA7 · UniProt O00311 · UniProt Q9UBU7 · UniProt P49736