Research workbench
Crystal complex of p53-V272M and antimony ion
Analyse Crystal complex of p53-V272M and antimony ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EAX
- Type
- protein
- Length
- 774 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Homo sapiens
- Molecule
- Cellular tumor antigen p53
- UniProt
- P04637
- Ligands
- ZN, SB
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.55 · 2 distinct chains · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cellular tumor antigen p53 | protein | 194 | 9% helix, 34% strand | P04637 |
| B, D | Cellular tumor antigen p53 | protein | 193 | 9% helix, 34% strand | P04637 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SB · Antimony (III) 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
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.71 | 0.75 | 129 | empty |
| 2 | 631 | 0.65 | 0.75 | 79 | empty |
| 3 | 69 | 0.44 | 0.82 | 21 | empty |
| 4 | 91 | 0.37 | 0.76 | 20 | empty |
| 5 | 76 | 0.37 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 604 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 590 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 193 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7EAX · Crystal complex of P53-V272M and antimony ion · 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 7EAX · PDBe 7EAX · UniProt P04637
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