› 5oai

X-ray diffraction
2Å resolution

Structure of MDM2 with low molecular weight inhibitor

Released:
DOI: 10.2210/pdb5oai/pdb
PDB entry 5oai coloured by chain, front view.
PDB entry 5oai coloured by chain, side view.
PDB entry 5oai coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A fluorinated indole-based MDM2 antagonist selectively inhibits the growth of p53wt osteosarcoma cells.
Skalniak L, Twarda-Clapa A, Neochoritis CG, Surmiak E, Machula M, Wisniewska A, Labuzek B, Ali AM, Krzanik S, Dubin G, Groves M, Dömling A, Holak TA
FEBS J 286 1360-1374 (2019)
PMID: 30715803

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169499 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase Mdm2 Chain: A
Molecule details ›
Chain: A
Length: 97 amino acids
Theoretical weight: 11.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 18-113; Coverage: 20%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain

Ligands and Environments

1 bound ligand:
Ligand B5K 1 x B5K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: I222
Unit cell:
a: 49.731Å b: 59.216Å c: 83.897Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.216 0.227
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation.
Márquez-Cantudo et al. (2021)
1 more

2 mentions without citation

Interfacial Peptides as Affinity Modulating Agents of Protein-Protein Interactions.
Ershov et al. (2022)
1 more