› 1gy3

X-ray diffraction
2.7Å resolution

pCDK2/cyclin A in complex with MgADP, nitrate and peptide substrate

Released:
DOI: 10.2210/pdb1gy3/pdb
PDB entry 1gy3 coloured by chain, front view.
PDB entry 1gy3 coloured by chain, side view.
PDB entry 1gy3 coloured by chain, top view.
Source organisms:
Primary publication:
Structural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism.
Cook A, Lowe ED, Chrysina ED, Skamnaki VT, Oikonomakos NG, Johnson LN
Biochemistry 41 7301-11 (2002)
PMID: 12044161

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148890 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Cyclin-dependent kinase 2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 299 amino acids
Theoretical weight: 34.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P24941 (Residues: 1-298; Coverage: 100%)
Gene names: CDK2, CDKN2
Sequence domains: Protein kinase domain
Structure domains:
Cyclin-A2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 258 amino acids
Theoretical weight: 29.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P20248 (Residues: 175-432; Coverage: 60%)
Gene names: CCN1, CCNA, CCNA2
Sequence domains:
Structure domains: Cyclin-like
SUBSTRATE PEPTIDE Chains: E, F
Molecule details ›
Chains: E, F
Length: 7 amino acids
Theoretical weight: 836 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ATP 2 x ATP
Ligand MG 2 x MG
Ligand NO3 2 x NO3
Ligand GOL 2 x GOL
1 modified residue:
Ligand TPO 2 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21212
Unit cell:
a: 150.71Å b: 164.1Å c: 72.43Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.25 0.313
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

The structural basis for control of eukaryotic protein kinases.
Endicott et al. (2012)
4 more

12 mentions without citation

Structural insights into the functional diversity of the CDK-cyclin family.
Wood et al. (2018)
11 more