MolNFT v1 · #126847 · protein + DNA
New insights into the role of DNA shape on its recognition by P53 proteins (complex P53DBD-GADD45)
5MF7 · Cellular tumor antigen P53: “New insights into the role of DNA shape on its recognition by P53 proteins (complex P53DBD-GADD45)”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.64). MolNFT v1 #126847 on GenesisL1…
- PDB
- 5MF7
- Type
- protein + DNA
- Length
- 396 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
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellular tumor antigen P53 | protein | 188 | 11% helix, 36% strand | P04637 |
| C | DNA | dna | 20 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.64 | 0.76 | 51 | empty |
| 2 | 109 | 0.39 | 0.75 | 21 | empty |
| 3 | 71 | 0.26 | 0.71 | 13 | empty |
| 4 | 57 | 0.25 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 622 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 110 Ų buried · 1 hydrogen bond · protein-nucleic
- B–C · 104 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5MF7 · 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 5MF7 · PDBe 5MF7 · UniProt P04637
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