Research workbench
Arsenic-bound P53 DNA-binding domain mutant V272M
Analyse Arsenic-bound P53 DNA-binding domain mutant V272M in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V97
- Type
- protein
- Length
- 773 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
- Pockets
- 14 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cellular tumor antigen P53 | protein | 194 | 8% helix, 34% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 193 | 8% helix, 34% strand | P04637 |
| D | Cellular tumor antigen P53 | protein | 192 | 8% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.57 | 0.77 | 40 | empty |
| 2 | 344 | 0.55 | 0.74 | 40 | empty |
| 3 | 301 | 0.53 | 0.75 | 49 | empty |
| 4 | 231 | 0.52 | 0.76 | 41 | empty |
| 5 | 251 | 0.50 | 0.74 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 594 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 223 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7V97 · Arsenic-bound p53 DNA-binding domain mutant V272M · 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 7V97 · PDBe 7V97 · UniProt P04637
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