› 6y4q

X-ray diffraction
1.63Å resolution

Structure of a stapled peptide bound to MDM2

Released:
DOI: 10.2210/pdb6y4q/pdb
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PDB entry 6y4q coloured by chain, front view.
PDB entry 6y4q coloured by chain, side view.
PDB entry 6y4q coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Diarylethene moiety as an enthalpy-entropy switch: photoisomerizable stapled peptides for modulating p53/MDM2 interaction.
Strizhak AV, Babii O, Afonin S, Bakanovich I, Pantelejevs T, Xu W, Fowler E, Eapen R, Sharma K, Platonov MO, Hurmach VV, Itzhaki L, Hyvönen M, Ulrich AS, Spring DR, Komarov IV
Org Biomol Chem 18 5359-5369 (2020)
PMID: 32390036

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-167831 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase Mdm2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 92 amino acids
Theoretical weight: 10.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q00987 (Residues: 17-108; Coverage: 19%)
  • Best match: Q00987-6 (Residues: 17-29)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
ACE-LEU-THR-PHE-GLY-GLU-TYR-TRP-ALA-GLN-LEU-ALA-SER Chains: C, D
Molecule details ›
Chains: C, D
Length: 13 amino acids
Theoretical weight: 1.41 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand O9E 2 x O9E
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P1
Unit cell:
a: 34.24Å b: 34.84Å c: 48.41Å
α: 93.38° β: 107.38° γ: 117.45°
R-values:
R R work R free
0.196 0.194 0.229
Expression systems:
  • Escherichia coli BL21
  • Not provided

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Citations

2 review citations

Molecular photoswitches in aqueous environments.
Volarić et al. (2021)
1 more

4 mentions without citation

Peptide-based inhibitors of protein-protein interactions: biophysical, structural and cellular consequences of introducing a constraint.
Wang et al. (2021)
3 more

PDB-REDO

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