Research workbench
Structure of the P53 cancer mutant Y220C with bound small-molecule stabilizer PHIKAN5149
Analyse Structure of the P53 cancer mutant Y220C with bound small-molecule stabilizer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ABA
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- UL7, ZN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 195 | 10% helix, 33% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 197 | 8% helix, 34% strand | P04637 |
Ligands and binding sites
- UL7 · 1-{1-[(3-bromo-5-chloro-2-hydroxyphenyl)methyl piperidin-4-yl}piperidin-4-ol] · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
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 | 476 | 0.66 | 0.78 | 52 | empty |
| 2 | 147 | 0.44 | 0.76 | 20 | empty |
| 3 | 59 | 0.39 | 0.80 | 15 | UL7 |
| 4 | 57 | 0.38 | 0.80 | 14 | UL7 |
| 5 | 103 | 0.37 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 302 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5ABA · Structure of the p53 cancer mutant Y220C with bound small-molecule stabilizer PhiKan5149 · 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 5ABA · PDBe 5ABA · UniProt P04637
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