› 4yc3

X-ray diffraction
2.7Å resolution

CDK1/CyclinB1/CKS2 Apo

Released:
DOI: 10.2210/pdb4yc3/pdb
PDB entry 4yc3 coloured by chain, front view.
PDB entry 4yc3 coloured by chain, side view.
PDB entry 4yc3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
CDK1 structures reveal conserved and unique features of the essential cell cycle CDK.
Brown NR, Korolchuk S, Martin MP, Stanley WA, Moukhametzianov R, Noble MEM, Endicott JA
Nat Commun 6 6769 (2015)
PMID: 25864384

Function and Biology Details

Reactions catalysed: 
ATP + a protein = ADP + a phosphoprotein
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139063 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Cyclin-dependent kinase 1 Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 34.55 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P06493 (Residues: 1-297; Coverage: 100%)
Gene names: CDC2, CDC28A, CDK1, CDKN1, P34CDC2
Sequence domains: Protein kinase domain
Structure domains:
G2/mitotic-specific cyclin-B1 Chain: B
Molecule details ›
Chain: B
Length: 273 amino acids
Theoretical weight: 31.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P14635 (Residues: 165-433; Coverage: 62%)
Gene names: CCNB, CCNB1
Sequence domains:
Structure domains: Cyclin-like
Cyclin-dependent kinases regulatory subunit 2 Chain: C
Molecule details ›
Chain: C
Length: 84 amino acids
Theoretical weight: 10.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P33552 (Residues: 1-79; Coverage: 100%)
Gene name: CKS2
Sequence domains: Cyclin-dependent kinase regulatory subunit
Structure domains: Cyclin-dependent kinase, regulatory subunit

Ligands and Environments

1 bound ligand:
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 69.2Å b: 70.15Å c: 156.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.211 0.26
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

9 review citations

Cyclin-dependent protein kinase inhibitors including palbociclib as anticancer drugs.
Roskoski R. (2016)
8 more

17 mentions without citation

Ubiquitin signaling in cell cycle control and tumorigenesis.
Dang et al. (2021)
16 more