› 4ud7

X-ray diffraction
1.6Å resolution

Structure of the stapled peptide YS-02 bound to MDM2

Released:
DOI: 10.2210/pdb4ud7/pdb
PDB entry 4ud7 coloured by chain, front view.
PDB entry 4ud7 coloured by chain, side view.
PDB entry 4ud7 coloured by chain, top view.
Source organisms:
Primary publication:
Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.
Tan YS, Reeks J, Brown CJ, Thean D, Ferrer Gago FJ, Yuen TY, Goh ET, Lee XE, Jennings CE, Joseph TL, Lakshminarayanan R, Lane DP, Noble ME, Verma CS
J Phys Chem Lett 7 3452-7 (2016)
PMID: 27532490

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-165215 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase Mdm2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 114 amino acids
Theoretical weight: 12.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q00987 (Residues: 17-125; Coverage: 22%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain
YS-02 Chains: F, G, H, I
Molecule details ›
Chains: F, G, H, I
Length: 16 amino acids
Theoretical weight: 1.84 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 46.148Å b: 69.538Å c: 78.464Å
α: 90° β: 102.36° γ: 90°
R-values:
R R work R free
0.14 0.138 0.178
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting.
Tan et al. (2019)
2 more

3 mentions without citation

Stapled Peptides Inhibitors: A New Window for Target Drug Discovery.
Ali et al. (2019)
2 more