› 3lnj

X-ray diffraction
2.4Å resolution

Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha)

Released:
DOI: 10.2210/pdb3lnj/pdb
PDB entry 3lnj coloured by chain, front view.
PDB entry 3lnj coloured by chain, side view.
PDB entry 3lnj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A left-handed solution to peptide inhibition of the p53-MDM2 interaction.
Liu M, Pazgier M, Li C, Yuan W, Li C, Lu W
Angew Chem Int Ed Engl 49 3649-52 (2010)
PMID: 20449836

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-163742 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
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 Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 12 amino acids
Theoretical weight: 1.52 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand SO4 1 x SO4
Ligand CL 1 x CL
Ligand GOL 1 x GOL
9 modified residues:
Ligand DTH 3 x DTH
Ligand DSG 6 x DSG
Ligand DTR 3 x DTR
Ligand DTY 3 x DTY
Ligand DAL 3 x DAL
Ligand DLE 9 x DLE
Ligand DGL 3 x DGL
Ligand DLY 3 x DLY
Ligand DAR 3 x DAR

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: C2221
Unit cell:
a: 68.976Å b: 213.478Å c: 45.536Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.209 0.255
Expression system: Not provided

Quick links

Citations

12 review citations

Peptide-based inhibitors of protein-protein interactions.
Wójcik et al. (2016)
11 more

7 mentions without citation

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