› 5z02

X-ray diffraction
1.35Å resolution

Crystal structure of HIS6-tagged Mdm2 with nutlin-3a

Released:
DOI: 10.2210/pdb5z02/pdb
PDB entry 5z02 coloured by chain, front view.
PDB entry 5z02 coloured by chain, side view.
PDB entry 5z02 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Su ZD, Cheng XY, Chen R, Pi N

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: 110 amino acids
Theoretical weight: 12.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q00987 (Residues: 24-112; Coverage: 18%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 42.5Å b: 42.99Å c: 54.53Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.226 0.254
Expression system: Escherichia coli BL21

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