› 3iwy

X-ray diffraction
1.93Å resolution

Crystal structure of human MDM2 complexed with D-peptide (12 residues)

Released:
DOI: 10.2210/pdb3iwy/pdb
PDB entry 3iwy coloured by chain, front view.
PDB entry 3iwy coloured by chain, side view.
PDB entry 3iwy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
D-peptide inhibitors of the p53-MDM2 interaction for targeted molecular therapy of malignant neoplasms.
Liu M, Li C, Pazgier M, Li C, Mao Y, Lv Y, Gu B, Wei G, Yuan W, Zhan C, Lu WY, Lu W
Proc Natl Acad Sci U S A 107 14321-6 (2010)
PMID: 20660730

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-163674 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
D-peptide inhibitor Chains: B, D
Molecule details ›
Chains: B, D
Length: 12 amino acids
Theoretical weight: 1.52 KDa
Source organism: Homo sapiens
Expression system: Not provided
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
UniProt:
  • Canonical: Q00987 (Residues: 25-109; Coverage: 17%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain

Ligands and Environments

No bound ligands
8 modified residues:
Ligand DAS 2 x DAS
Ligand DTR 4 x DTR
Ligand DPR 2 x DPR
Ligand DLE 6 x DLE
Ligand DAL 4 x DAL
Ligand DPN 2 x DPN
Ligand DGL 2 x DGL
Ligand DAR 2 x DAR

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 33.569Å b: 46.503Å c: 49.353Å
α: 90° β: 92.35° γ: 90°
R-values:
R R work R free
0.213 0.21 0.259
Expression system: Not provided

Quick links

Citations

30 review citations

MDM2, MDMX and p53 in oncogenesis and cancer therapy.
Wade et al. (2013)
29 more

7 mentions without citation

Targeting p53-MDM2-MDMX loop for cancer therapy.
Zhang et al. (2014)
6 more