› 5afg

X-ray diffraction
1.9Å resolution

Structure of the Stapled Peptide Bound to Mdm2

Released:
DOI: 10.2210/pdb5afg/pdb
PDB entry 5afg coloured by chain, front view.
PDB entry 5afg coloured by chain, side view.
PDB entry 5afg coloured by chain, top view.
Source organisms:
Primary publication:
Double Strain-Promoted Macrocyclization for the Rapid Selection of Cell-Active Stapled Peptides.
Lau YH, Wu Y, Rossmann M, Tan BX, de Andrade P, Tan YS, Verma C, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR
Angew Chem Int Ed Engl 54 15410-3 (2015)
PMID: 26768531

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165433 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase Mdm2 Chain: A
Molecule details ›
Chain: A
Length: 97 amino acids
Theoretical weight: 11.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q00987 (Residues: 17-108; Coverage: 19%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain
STAPLED PEPTIDE Chain: B
Molecule details ›
Chain: B
Length: 12 amino acids
Theoretical weight: 1.44 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand P07 1 x P07
1 modified residue:
Ligand LAY 1 x LAY

Experiments and Validation Details

Entry percentile scores
Spacegroup: P41212
Unit cell:
a: 36.821Å b: 36.821Å c: 177.416Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.176 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

8 review citations

New Modalities for Challenging Targets in Drug Discovery.
Valeur et al. (2017)
7 more

6 mentions without citation

Stapled Peptides Inhibitors: A New Window for Target Drug Discovery.
Ali et al. (2019)
5 more