Research workbench
Crystal structure of the P53 cancer mutant Y220C in complex with a monofluorinated derivative of the small molecule stabilizer PHIKAN083
Analyse Crystal structure of the P53 cancer mutant Y220C in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G4M
- 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
- O82, ZN
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 195 | 9% helix, 33% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 197 | 8% helix, 33% strand | P04637 |
Ligands and binding sites
- O82 · 1-[9-(2-fluoroethyl)-9H-carbazol-3-yl]-N-methylmethanamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
- EDO · 1,2-ethanediol · additive · chains 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 | 497 | 0.65 | 0.77 | 55 | empty |
| 2 | 137 | 0.42 | 0.75 | 19 | empty |
| 3 | 56 | 0.40 | 0.81 | 15 | O82 |
| 4 | 57 | 0.39 | 0.80 | 19 | O82 |
| 5 | 94 | 0.37 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 286 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5G4M · Crystal structure of the p53 cancer mutant Y220C in complex with a monofluorinated… · 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 5G4M · PDBe 5G4M · UniProt P04637
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