› 3mks

X-ray diffraction
2.6Å resolution

Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2

Released:
DOI: 10.2210/pdb3mks/pdb
PDB entry 3mks coloured by chain, front view.
PDB entry 3mks coloured by chain, side view.
PDB entry 3mks coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
An allosteric inhibitor of substrate recognition by the SCF(Cdc4) ubiquitin ligase.
Orlicky S, Tang X, Neduva V, Elowe N, Brown ED, Sicheri F, Tyers M
Nat Biotechnol 28 733-7 (2010)
PMID: 20581844

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139781 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Suppressor of kinetochore protein 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 169 amino acids
Theoretical weight: 19.5 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P52286 (Residues: 2-194; Coverage: 85%)
Gene names: CBF3D, D9798.14, SKP1, YDR328C
Sequence domains:
Structure domains: Potassium Channel Kv1.1; Chain A
Cell division control protein 4 Chains: B, D
Molecule details ›
Chains: B, D
Length: 464 amino acids
Theoretical weight: 52.86 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P07834 (Residues: 263-744; Coverage: 59%)
Gene names: CDC4, YFL009W
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 11 x SO4
Ligand C1C 1 x C1C
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P32
Unit cell:
a: 108.281Å b: 108.281Å c: 165.594Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.213 0.211 0.266
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

50 review citations

Ubiquitin Ligases: Structure, Function, and Regulation.
Zheng et al. (2017)
49 more

6 mentions without citation

Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation.
Bulatov et al. (2015)
5 more