Structural basis of reactivation of oncogenic P53 mutants by a small molecule: methylene quinuclidinone (mq). human P53DBD-R273H mutant bound to DNA and mq: R273H-DNA-mq

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 35% strand (DSSP).

Ligands and binding sites

• QN8 · (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one · ligand · 2 copies · chains A, B
• QNN · (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one · ligand · 2 copies · chains A, C, B
• ZN · Zinc ion · metal · 2 copies · chains A, B
• FMT · Formic acid · additive · 24 copies · chains A, C, B
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
• ACT · Acetate ion · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 591 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 222 Ų buried · 6 hydrogen bonds · protein-nucleic
• A–C · 193 Ų buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 7B49 · Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P04637
• Elsewhere: RCSB PDB 7B49 · PDBe 7B49 · UniProt P04637