MolNFT v1 · #149991 · protein
Structure of the P53 cancer mutant Y220C in complex with small- molecule stabilizer PK9328
6GGF · Cellular tumor antigen P53: “Structure of the P53 cancer mutant Y220C in complex with small- molecule stabilizer PK9328”. X-ray diffraction, 2 ligands (EXQ, ZN), 5 pockets (best druggability 0.65). MolNFT v1 #149991 on GenesisL1: 3D…
- PDB
- 6GGF
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- EXQ, ZN
- Pockets
- 5 · best druggability 0.65
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 | 196 | 10% helix, 33% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 198 | 8% helix, 33% strand | P04637 |
Ligands and binding sites
- EXQ · [9-ethyl-7-(4-methylthiophen-2-yl)carbazol-3-yl]methyl-methyl-azanium · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · 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 | 478 | 0.65 | 0.77 | 53 | empty |
| 2 | 133 | 0.43 | 0.76 | 20 | empty |
| 3 | 70 | 0.42 | 0.80 | 18 | EXQ |
| 4 | 66 | 0.41 | 0.80 | 19 | EXQ |
| 5 | 90 | 0.37 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 293 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6GGF · Structure of the p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9328 · 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 6GGF · PDBe 6GGF · UniProt P04637
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