Research workbench
An induced fit mechanism regulates P53 DNA binding kinetics to confer sequence specificity
Analyse An induced fit mechanism regulates P53 DNA binding kinetics to confer sequence… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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