› 3jzs

X-ray diffraction
1.78Å resolution

Human MDM2 liganded with a 12mer peptide inhibitor (pDIQ)

Released:
DOI: 10.2210/pdb3jzs/pdb
PDB entry 3jzs coloured by chain, front view.
PDB entry 3jzs coloured by chain, side view.
PDB entry 3jzs coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based design of high affinity peptides inhibiting the interaction of p53 with MDM2 and MDMX.
Phan J, Li Z, Kasprzak A, Li B, Sebti S, Guida W, Schönbrunn E, Chen J
J Biol Chem 285 2174-83 (2010)
PMID: 19910468

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-163695 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase Mdm2 Chain: A
Molecule details ›
Chain: A
Length: 86 amino acids
Theoretical weight: 10.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 24-109; Coverage: 18%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain
pDIQ peptide (12mer) Chain: P
Molecule details ›
Chain: P
Length: 12 amino acids
Theoretical weight: 1.56 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21212
Unit cell:
a: 43.81Å b: 50.593Å c: 39.204Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.253
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

Drugging the p53 pathway: understanding the route to clinical efficacy.
Khoo et al. (2014)
12 more

10 mentions without citation

Interfacial Peptides as Affinity Modulating Agents of Protein-Protein Interactions.
Ershov et al. (2022)
9 more