› 5swk

X-ray diffraction
1.92Å resolution

Crystal structure of p53 epitope-scaffold based on a inhibitor of cysteine proteases in complex with human MDM2

Released:
DOI: 10.2210/pdb5swk/pdb
PDB entry 5swk coloured by chain, front view.
PDB entry 5swk coloured by chain, side view.
PDB entry 5swk coloured by chain, top view.
Source organisms:
Primary publication:
Mimicking a p53-MDM2 interaction based on a stable immunoglobulin-like domain scaffold.
Jimenez-Sandoval P, Madrigal-Carrillo EA, Santamaría-Suárez HA, Maturana D, Rentería-González I, Benitez-Cardoza CG, Torres-Larios A, Brieba LG
Proteins 86 802-812 (2018)
PMID: 29696695

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-166088 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase Mdm2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 153 amino acids
Theoretical weight: 17.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 1-150; Coverage: 31%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain
De novo protein based on the inhibitor Amoebiasin-1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 110 amino acids
Theoretical weight: 12.04 KDa
Source organism: Entamoeba histolytica
Expression system: Escherichia coli

Ligands and Environments

3 bound ligands:
Ligand CL 7 x CL
Ligand SO4 2 x SO4
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P43212
Unit cell:
a: 87.361Å b: 87.361Å c: 160.84Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.221 0.249
Expression system: Escherichia coli

Quick links

Citations

3 mentions without citation

Insights into the Allergenic Potential of the Edible Yellow Mealworm (Tenebrio molitor).
Barre et al. (2019)
2 more