Research workbench
Human p53 core domain with hot spot mutation R282W in complex with the natural CDKN1A(p21) p53-response element and Arsenic
Analyse Human p53 core domain with hot spot mutation R282W in complex with the natural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EEU
- Type
- protein + DNA
- Length
- 1,703 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Cellular tumor antigen p53; CDKN1A(p21) sense strand; CDKN1A(p21) anti-sense strand
- UniProt
- P04637
- Ligands
- ARS, ZN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.9 · 4 distinct chains · 12% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H | Cellular tumor antigen p53 | protein | 198 | 12% helix, 33% strand | P04637 |
| F | Cellular tumor antigen p53 | protein | 197 | 12% helix, 34% strand | P04637 |
| I, K | CDKN1A(p21) sense strand | dna | 30 | — | — |
| J, L | CDKN1A(p21) anti-sense strand | dna | 30 | — | — |
Ligands and binding sites
- ARS · Arsenic · metal · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.76 | 0.79 | 92 | empty |
| 2 | 1056 | 0.75 | 0.78 | 81 | empty |
| 3 | 818 | 0.75 | 0.80 | 73 | empty |
| 4 | 796 | 0.74 | 0.79 | 72 | empty |
| 5 | 601 | 0.71 | 0.79 | 54 | empty |
Interfaces
32 interfaces between chains.
- K–L · 1363 Ų buried · 151 hydrogen bonds · nucleic-nucleic
- I–J · 1350 Ų buried · 158 hydrogen bonds · nucleic-nucleic
- C–G · 957 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 948 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 513 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7EEU · Human P53 core domain with hot spot mutation R282W in complex with the natural… · 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 7EEU · PDBe 7EEU · UniProt P04637
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