› 4i3z

X-ray diffraction
2.05Å resolution

Structure of pCDK2/CyclinA bound to ADP and 2 Magnesium ions

Released:
DOI: 10.2210/pdb4i3z/pdb
PDB entry 4i3z coloured by chain, front view.
PDB entry 4i3z coloured by chain, side view.
PDB entry 4i3z coloured by chain, top view.
Source organisms:
Primary publication:
Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase.
Jacobsen DM, Bao ZQ, O'Brien P, Brooks CL, Young MA
J Am Chem Soc 134 15357-70 (2012)
PMID: 22891849

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150316 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cyclin-dependent kinase 2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 296 amino acids
Theoretical weight: 33.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P24941 (Residues: 1-296; Coverage: 99%)
Gene names: CDK2, CDKN2
Sequence domains: Protein kinase domain
Structure domains:
Cyclin-A2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 257 amino acids
Theoretical weight: 29.41 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P51943 (Residues: 165-421; Coverage: 61%)
Gene names: Ccna, Ccna2, Cyca, Cyca2
Sequence domains:
Structure domains: Cyclin-like

Ligands and Environments

4 bound ligands:
Ligand ADP 2 x ADP
Ligand MG 4 x MG
Ligand GOL 9 x GOL
Ligand CL 2 x CL
1 modified residue:
Ligand TPO 2 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21
Unit cell:
a: 70.77Å b: 164.13Å c: 73.28Å
α: 90° β: 107.07° γ: 90°
R-values:
R R work R free
0.199 0.197 0.228
Expression system: Escherichia coli BL21

Quick links

Citations

7 review citations

Src protein-tyrosine kinase structure, mechanism, and small molecule inhibitors.
Roskoski R. (2015)
6 more

2 mentions without citation

Determining the Functions of HIV-1 Tat and a Second Magnesium Ion in the CDK9/Cyclin T1 Complex: A Molecular Dynamics Simulation Study.
Jin et al. (2015)
1 more