Research workbench
Structural basis of reactivation of oncogenic P53 mutants by a small molecule: methylene quinuclidinone (mq). human P53DBD-R273H mutant bound to DNA: R273H-DNA
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
- 7B4A
- Type
- protein + DNA
- Length
- 410 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; DNA target
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellular tumor antigen P53 | protein | 195 | 12% helix, 35% strand | P04637 |
| C | DNA target | dna | 20 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.65 | 0.77 | 51 | empty |
| 2 | 107 | 0.40 | 0.76 | 21 | empty |
| 3 | 69 | 0.33 | 0.76 | 18 | empty |
| 4 | 62 | 0.32 | 0.76 | 20 | empty |
| 5 | 100 | 0.31 | 0.72 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 561 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 324 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 7B4A · 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 7B4A · PDBe 7B4A · UniProt P04637
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.