› 6ya6

X-ray diffraction
1.44Å resolution

Minimal construct of Cdc7-Dbf4 bound to XL413

Released:
DOI: 10.2210/pdb6ya6/pdb
PDB entry 6ya6 coloured by chain, front view.
PDB entry 6ya6 coloured by chain, side view.
PDB entry 6ya6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase.
Dick SD, Federico S, Hughes SM, Pye VE, O'Reilly N, Cherepanov P
Structure 28 954-962.e4 (2020)
PMID: 32521228

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126244 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cell division cycle 7-related protein kinase Chain: A
Molecule details ›
Chain: A
Length: 359 amino acids
Theoretical weight: 40.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O00311 (Residues: 37-467, 534-574; Coverage: 62%)
Gene names: CDC7, CDC7L1
Sequence domains: Protein kinase domain
Protein DBF4 homolog A Chain: B
Molecule details ›
Chain: B
Length: 144 amino acids
Theoretical weight: 17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBU7 (Residues: 210-350; Coverage: 21%)
Gene names: ASK, DBF4, DBF4A, ZDBF1
Sequence domains: DBF zinc finger

Ligands and Environments

6 bound ligands:
Ligand 0SX 1 x 0SX
Ligand ZN 2 x ZN
Ligand PEG 1 x PEG
Ligand BO3 1 x BO3
Ligand CL 1 x CL
Ligand IMD 1 x IMD
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P41212
Unit cell:
a: 61.64Å b: 61.64Å c: 233.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.167 0.193
Expression system: Escherichia coli

Quick links

Citations

1 review citation

CDC7 as a novel biomarker and druggable target in cancer.
Liu et al. (2022)
7 other articles

1 mention without citation

Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase.
Dick et al. (2020)