PDBe 4ud7

X-ray diffraction
1.6Å resolution

Structure of the stapled peptide YS-02 bound to MDM2

Released:

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
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (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%)
  • Best match: Q00987-8 (Residues: 1-64)
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