Research workbench
Structural basis of reactivation of oncogenic P53 mutants by a small molecule: methylene quinuclidinone (mq). human P53DBD-R282W mutant bound to DNA: R282W-mq (II)
Analyse Structural basis of reactivation of oncogenic P53 mutants by a small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B4G
- Type
- protein + DNA
- Length
- 209 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; DNA target
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 198 | 12% helix, 33% strand | P04637 |
| B | DNA target | dna | 11 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.37 | 0.76 | 20 | empty |
| 2 | 64 | 0.27 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 242 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 7B4G · 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 7B4G · PDBe 7B4G · UniProt P04637
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