› 5c5a

X-ray diffraction
1.15Å resolution

Crystal Structure of HDM2 in complex with Nutlin-3a

Released:
DOI: 10.2210/pdb5c5a/pdb
PDB entry 5c5a coloured by chain, front view.
PDB entry 5c5a coloured by chain, side view.
PDB entry 5c5a coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Orts J, Waelti MA, Marsh M, Vera L, Gossert AD, Guentert P, Riek R

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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 92 amino acids
Theoretical weight: 10.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 20-111; Coverage: 19%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain

Ligands and Environments

4 bound ligands:
Ligand NUT 2 x NUT
Ligand SO4 2 x SO4
Ligand CL 2 x CL
Ligand IOD 4 x IOD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 41.62Å b: 43.63Å c: 52.67Å
α: 90° β: 90.04° γ: 90°
R-values:
R R work R free
0.154 0.153 0.168
Expression system: Escherichia coli

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