Research workbench
Arsenic-bound P53 DNA-binding domain mutant G245S
Analyse Arsenic-bound P53 DNA-binding domain mutant G245S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DHY
- Type
- protein
- Length
- 777 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- ARS, ZN, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 193 | 9% helix, 34% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 196 | 9% helix, 33% strand | P04637 |
| C, D | Cellular tumor antigen P53 | protein | 194 | 9% helix, 34% strand | P04637 |
Ligands and binding sites
- ARS · Arsenic · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains D
- GOL · Glycerol · additive · 7 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.70 | 0.76 | 103 | GOL |
| 2 | 671 | 0.66 | 0.75 | 79 | empty |
| 3 | 342 | 0.61 | 0.78 | 43 | empty |
| 4 | 117 | 0.42 | 0.76 | 22 | GOL |
| 5 | 100 | 0.40 | 0.77 | 21 | empty |
Interfaces
5 interfaces between chains.
- B–D · 645 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 608 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 419 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 268 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7DHY · Arsenic-bound p53 DNA-binding domain mutant G245S · 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 7DHY · PDBe 7DHY · UniProt P04637
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