› 5zxf

X-ray diffraction
1.25Å resolution

The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a

Released:
DOI: 10.2210/pdb5zxf/pdb
PDB entry 5zxf coloured by chain, front view.
PDB entry 5zxf coloured by chain, side view.
PDB entry 5zxf coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Cheng XY, Su ZD, Pi N, Cao CZ, Zhao ZT, Zhou JJ, Chen R, Kuang ZK, Huang YQ

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: 87 amino acids
Theoretical weight: 10.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q00987 (Residues: 24-110; 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: 42.575Å b: 43.222Å c: 53.853Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.218 0.243
Expression system: Escherichia coli K-12

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