MolNFT v1 · #149988 · protein
P53 cancer mutant Y220C in complex with small-molecule stabilizer PK9320
6GGC · Cellular tumor antigen P53: “P53 cancer mutant Y220C in complex with small-molecule stabilizer PK9320”. X-ray diffraction, 2 ligands (EXN, ZN), 6 pockets (best druggability 0.66). MolNFT v1 #149988 on GenesisL1: 3D structure…
- PDB
- 6GGC
- Type
- protein
- Length
- 395 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- EXN, ZN
- Pockets
- 6 · best druggability 0.66
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 | 197 | 9% helix, 33% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 198 | 8% helix, 33% strand | P04637 |
Ligands and binding sites
- EXN · [9-ethyl-7-(furan-2-yl)carbazol-3-yl]methyl-methyl-azanium · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.66 | 0.78 | 54 | EDO |
| 2 | 138 | 0.43 | 0.75 | 21 | empty |
| 3 | 64 | 0.41 | 0.80 | 16 | EXN |
| 4 | 69 | 0.40 | 0.79 | 19 | EXN |
| 5 | 91 | 0.37 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 339 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GGC · p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9320 · 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 6GGC · PDBe 6GGC · UniProt P04637
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