› 3lnz

X-ray diffraction
1.95Å resolution

Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant)

Released:
DOI: 10.2210/pdb3lnz/pdb
PDB entry 3lnz coloured by chain, front view.
PDB entry 3lnz coloured by chain, side view.
PDB entry 3lnz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Systematic mutational analysis of peptide inhibition of the p53-MDM2/MDMX interactions.
Li C, Pazgier M, Li C, Yuan W, Liu M, Wei G, Lu WY, Lu W
J Mol Biol 398 200-13 (2010)
PMID: 20226197

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-163743 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase Mdm2 Chains: A, C, E, G, I, K, M, O
Molecule details ›
Chains: A, C, E, G, I, K, M, O
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
12-mer peptide inhibitor Chains: B, D, F, H, J, L, N, P
Molecule details ›
Chains: B, D, F, H, J, L, N, P
Length: 12 amino acids
Theoretical weight: 1.38 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CL 8 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P3212
Unit cell:
a: 90.544Å b: 90.544Å c: 196.837Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.222 0.22 0.267
Expression system: Not provided

Quick links

Citations

6 review citations

Drugging the p53 pathway: understanding the route to clinical efficacy.
Khoo et al. (2014)
5 more

8 mentions without citation

Molecular dynamic simulation insights into the normal state and restoration of p53 function.
Fu et al. (2012)
7 more