PDBe 3iux

X-ray diffraction
1.65Å resolution

Crystal structure of human MDM2 in complex with a potent miniature protein inhibitor (18-residues)

Source organism: Homo sapiens
Primary publication:
Apamin as a template for structure-based rational design of potent peptide activators of p53.
Angew. Chem. Int. Ed. Engl. 48 8712-5 (2009)
PMID: 19827079

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
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase Mdm2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 85 amino acids
Theoretical weight: 10.04 KDa
Source organism: Homo sapiens
Expression system: Not provided
  • Canonical: Q00987 (Residues: 25-109; Coverage: 17%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain
miniature protein inhibitor Chains: B, D
Molecule details ›
Chains: B, D
Length: 18 amino acids
Theoretical weight: 2.22 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P212121
Unit cell:
a: 44.156Å b: 71.569Å c: 75.599Å
α: 90° β: 90° γ: 90°
R R work R free
0.186 0.185 0.206
Expression system: Not provided