MolNFT v1 · #30916 · protein + DNA
Structural basis of DNA recognition by P53 tetramers (complex IV)
2ADY · 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3': “Structural basis of DNA recognition by P53 tetramers (complex IV)”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.72). MolNFT v1 #30916 on GenesisL1: 3D structure…
- PDB
- 2ADY
- Type
- protein + DNA
- Length
- 419 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'; Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3' | dna | 12 | — | — |
| A | Cellular tumor antigen P53 | protein | 197 | 7% helix, 34% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 198 | 7% helix, 34% strand | P04637 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
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 | 535 | 0.72 | 0.81 | 49 | empty |
| 2 | 171 | 0.44 | 0.75 | 23 | empty |
| 3 | 116 | 0.40 | 0.75 | 19 | empty |
| 4 | 93 | 0.38 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- E–F · 525 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- F–A · 363 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 346 Ų buried · 2 hydrogen bonds · protein-protein
- E–B · 342 Ų buried · 7 hydrogen bonds · protein-nucleic
- F–B · 292 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 2ADY · Structural Basis of DNA Recognition by p53 Tetramers (complex IV) · the same entry in another collection · chain E against E, 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 2ADY · PDBe 2ADY · UniProt P04637
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