PDBe 3tpx

X-ray diffraction
1.8Å resolution

Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide inhibitor

Released:
Source organism: Homo sapiens
Primary publication:
An Ultrahigh Affinity D-Peptide Antagonist Of MDM2.
J. Med. Chem. (2012)
PMID: 22694121

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:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase Mdm2 Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 85 amino acids
Theoretical weight: 10.04 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q00987 (Residues: 25-109; Coverage: 17%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain
D-peptide inhibitor DPMI-delta Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 12 amino acids
Theoretical weight: 1.58 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2221
Unit cell:
a: 70.532Å b: 211.811Å c: 45.327Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.198 0.231
Expression system: Not provided