MolNFT v1 · #75766 · protein + DNA
An induced fit mechanism regulates P53 DNA binding kinetics to confer sequence specificity
3Q05 · Cellular tumor antigen P53: “An induced fit mechanism regulates P53 DNA binding kinetics to confer sequence specificity”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.71). MolNFT v1 #75766 on GenesisL1: 3D…
- PDB
- 3Q05
- Type
- protein + DNA
- Length
- 988 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; DNA (26-mer)
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, B | Cellular tumor antigen P53 | protein | 234 | 16% helix, 31% strand | P04637 |
| K | DNA (26-mer) | dna | 26 | — | — |
| L | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.71 | 0.89 | 20 | empty |
| 2 | 480 | 0.71 | 0.81 | 65 | empty |
| 3 | 171 | 0.69 | 0.89 | 21 | empty |
| 4 | 428 | 0.69 | 0.81 | 51 | empty |
| 5 | 353 | 0.61 | 0.78 | 45 | empty |
Interfaces
13 interfaces between chains.
- A–C · 2035 Ų buried · 32 hydrogen bonds · protein-protein
- D–B · 1922 Ų buried · 27 hydrogen bonds · protein-protein
- K–L · 1137 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- C–D · 390 Ų buried · 1 hydrogen bond · protein-protein
- D–L · 365 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3Q05 · An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity · 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 3Q05 · PDBe 3Q05 · UniProt P04637
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