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Structural basis of reactivation of oncogenic P53 mutants by a small molecule: methylene quinuclidinone (mq). human P53DBD-R273H mutant bound to mq: R273H-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
- 7B48
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- QNN, ZN
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 192 | 8% helix, 35% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 193 | 8% helix, 34% strand | P04637 |
| C | Cellular tumor antigen P53 | protein | 192 | 6% helix, 35% strand | P04637 |
| D | Cellular tumor antigen P53 | protein | 189 | 7% helix, 35% strand | P04637 |
Ligands and binding sites
- QNN · (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one · ligand · 2 copies · chains B, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.67 | 0.77 | 73 | ACT, EDO |
| 2 | 554 | 0.64 | 0.76 | 73 | empty |
| 3 | 313 | 0.52 | 0.74 | 37 | EDO |
| 4 | 73 | 0.44 | 0.81 | 16 | empty |
| 5 | 56 | 0.42 | 0.82 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–C · 560 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 496 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 472 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 144 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7B48 · 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 7B48 · PDBe 7B48 · UniProt P04637
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