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Structure of P63 DNA binding domain in complex with a 22 base pair A/T rich response element containing 2 base pair spacer between half sites
Analyse Structure of P63 DNA binding domain in complex with a 22 base pair A/T rich… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QYN
- Type
- protein + DNA
- Length
- 818 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor protein 63; 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*AP*TP…
- UniProt
- Q9H3D4
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor protein 63 | protein | 195 | 8% helix, 34% strand | Q9H3D4 |
| B | Tumor protein 63 | protein | 193 | 9% helix, 34% strand | Q9H3D4 |
| C | Tumor protein 63 | protein | 196 | 8% helix, 34% strand | Q9H3D4 |
| D | Tumor protein 63 | protein | 190 | 8% helix, 35% strand | Q9H3D4 |
| E, F | 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*AP*TP *GP*TP*TP*T)-3' | dna | 22 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.77 | 0.81 | 80 | empty |
| 2 | 853 | 0.74 | 0.79 | 71 | empty |
| 3 | 138 | 0.46 | 0.77 | 20 | empty |
| 4 | 117 | 0.42 | 0.77 | 20 | empty |
| 5 | 103 | 0.41 | 0.77 | 17 | empty |
Interfaces
11 interfaces between chains.
- E–F · 967 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- A–E · 298 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–F · 297 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–E · 295 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–F · 293 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3QYN · Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9H3D4 · AlphaFold monomer V2.0 prediction for tumor protein 63 (Q9H3D4) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9H3D4
- Elsewhere: RCSB PDB 3QYN · PDBe 3QYN · UniProt Q9H3D4
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