Research workbench
New insights into the role of DNA shape on its recognition by P53 proteins (complex P53DBD-LWC1)
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
- 5MCV
- Type
- protein + DNA
- Length
- 420 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; DNA
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellular tumor antigen P53 | protein | 200 | 11% helix, 34% strand | P04637 |
| C | DNA | dna | 20 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.66 | 0.77 | 50 | empty |
| 2 | 153 | 0.41 | 0.74 | 27 | empty |
| 3 | 89 | 0.36 | 0.75 | 20 | empty |
| 4 | 84 | 0.34 | 0.75 | 15 | EDO |
| 5 | 83 | 0.34 | 0.75 | 17 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 613 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 330 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5MCV · 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 5MCV · PDBe 5MCV · UniProt P04637
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