MolNFT v1 · #126769 · protein + DNA
New insights into the role of DNA shape on its recognition by P53 proteins (complex P53DBD-LHG1)
5MCT · Cellular tumor antigen P53: “New insights into the role of DNA shape on its recognition by P53 proteins (complex P53DBD-LHG1)”. X-ray diffraction, 2 ligands (FOR, ZN), 6 pockets (best druggability 0.65). MolNFT v1 #126769 on…
- PDB
- 5MCT
- 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
- FOR, ZN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellular tumor antigen P53 | protein | 200 | 10% helix, 34% strand | P04637 |
| C | DNA | dna | 20 | — | — |
Ligands and binding sites
- FOR · Formyl group · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.65 | 0.77 | 50 | empty |
| 2 | 168 | 0.41 | 0.73 | 25 | empty |
| 3 | 53 | 0.37 | 0.80 | 15 | EDO |
| 4 | 94 | 0.36 | 0.75 | 18 | EDO |
| 5 | 85 | 0.36 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 590 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 317 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 317 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5MCT · 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 5MCT · PDBe 5MCT · UniProt P04637
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