› 7na1

X-ray diffraction
2.3Å resolution

HDM2 in complex with compound 2

Released:
DOI: 10.2210/pdb7na1/pdb
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PDB entry 7na1 coloured by chain, front view.
PDB entry 7na1 coloured by chain, side view.
PDB entry 7na1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of
Reutershan MH, Machacek MR, Altman MD, Bogen S, Cai M, Cammarano C, Chen D, Christopher M, Cryan J, Daublain P, Fradera X, Geda P, Goldenblatt P, Hill AD, Kemper RA, Kutilek V, Li C, Martinez M, McCoy M, Nair L, Pan W, Thompson CF, Scapin G, Shizuka M, Spatz ML, Steinhuebel D, Sun B, Voss ME, Wang X, Yang L, Yeh TC, Dussault I, Marshall CG, Trotter BW
J Med Chem 64 16213-16241 (2021)
PMID: 34714078

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: 109 amino acids
Theoretical weight: 12.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 17-125; Coverage: 22%)
  • Best match: Q00987-6 (Residues: 17-29)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain

Ligands and Environments

4 bound ligands:
Ligand 1GI 2 x 1GI
Ligand SO4 1 x SO4
Ligand CIT 1 x CIT
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 39.349Å b: 39.432Å c: 160.389Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.26 0.255 0.354
Expression system: Escherichia coli

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Citations

2 review citations

Therapeutic Strategies to Activate p53.
Aguilar et al. (2022)
1 more

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