Research workbench
New insights into the role of DNA shape on its recognition by P53 proteins (complex P53DBD-agg-hg)
Analyse New insights into the role of DNA shape on its recognition by P53 proteins… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FJ5
- Type
- protein + DNA
- Length
- 836 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; DNA
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cellular tumor antigen P53 | protein | 199 | 9% helix, 35% strand | P04637 |
| F, G | DNA | dna | 20 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.76 | 0.80 | 87 | EDO |
| 2 | 781 | 0.75 | 0.80 | 68 | EDO |
| 3 | 274 | 0.60 | 0.79 | 33 | EDO |
| 4 | 299 | 0.59 | 0.78 | 34 | EDO |
| 5 | 460 | 0.58 | 0.74 | 55 | EDO |
Interfaces
13 interfaces between chains.
- F–G · 959 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- A–B · 492 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 488 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 367 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 337 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6FJ5 · New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex… · 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 6FJ5 · PDBe 6FJ5 · UniProt P04637
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