› 3tpx

X-ray diffraction
1.8Å resolution

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

Released:
DOI: 10.2210/pdb3tpx/pdb
PDB entry 3tpx coloured by chain, front view.
PDB entry 3tpx coloured by chain, side view.
PDB entry 3tpx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An ultrahigh affinity d-peptide antagonist Of MDM2.
Zhan C, Zhao L, Wei X, Wu X, Chen X, Yuan W, Lu WY, Pazgier M, Lu W
J Med Chem 55 6237-41 (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
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164084 (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

3 bound ligands:
Ligand SO4 3 x SO4
Ligand CL 5 x CL
Ligand ACT 4 x ACT
9 modified residues:
Ligand DTH 3 x DTH
Ligand DAL 6 x DAL
Ligand DTR 3 x DTR
Ligand DTY 3 x DTY
Ligand DSG 3 x DSG
Ligand DGL 3 x DGL
Ligand DLY 3 x DLY
Ligand DLE 6 x DLE
Ligand DAR 3 x DAR

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

Quick links

Citations

12 review citations

Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes.
Pelay-Gimeno et al. (2015)
11 more

7 mentions without citation

How To Design a Successful p53-MDM2/X Interaction Inhibitor: A Thorough Overview Based on Crystal Structures.
Estrada-Ortiz et al. (2016)
6 more