MolNFT v1 · #163930 · protein
P53 cancer mutant Y220S in complex with small-molecule stabilizer PK9301
6SI3 · Cellular tumor antigen P53: “P53 cancer mutant Y220S in complex with small-molecule stabilizer PK9301”. X-ray diffraction, 2 ligands (LEB, ZN), 7 pockets (best druggability 0.60). MolNFT v1 #163930 on GenesisL1: 3D structure…
- PDB
- 6SI3
- 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
- LEB, ZN
- Pockets
- 7 · best druggability 0.60
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 | 197 | 10% helix, 33% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 198 | 8% helix, 33% strand | P04637 |
Ligands and binding sites
- LEB · 1-[7-bromanyl-9-[2,2,2-tris(fluoranyl)ethyl]carbazol-3-yl]-~{N}-methyl-methanamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.60 | 0.78 | 33 | EDO |
| 2 | 129 | 0.45 | 0.77 | 25 | empty |
| 3 | 74 | 0.43 | 0.81 | 19 | LEB |
| 4 | 76 | 0.43 | 0.80 | 19 | LEB |
| 5 | 135 | 0.42 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 326 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SI3 · p53 cancer mutant Y220S in complex with small-molecule stabilizer PK9301 · 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 6SI3 · PDBe 6SI3 · UniProt P04637
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