Research workbench
Crystal structure of vitamin D receptor and 9-cis retinoic acid receptor DNA-binding domains bound to a DR3 response element
Analyse Crystal structure of vitamin D receptor and 9-cis retinoic acid receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YNW
- Type
- protein + DNA
- Length
- 205 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*AP*A) -3'…
- UniProt
- P11473, P19793
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*TP*TP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*AP*A) -3' | dna | 18 | — | — |
| D | 5'-D(*TP*TP*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*A) -3' | dna | 18 | — | — |
| A | Vitamin D3 receptor | protein | 96 | 44% helix, 6% strand | P11473 |
| B | Retinoic acid receptor rxr-alpha | protein | 73 | 29% helix, 5% strand | P19793 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.48 | 0.73 | 30 | empty |
| 2 | 85 | 0.42 | 0.79 | 20 | empty |
| 3 | 117 | 0.40 | 0.76 | 22 | empty |
| 4 | 103 | 0.34 | 0.73 | 12 | empty |
| 5 | 52 | 0.29 | 0.76 | 13 | empty |
Interfaces
5 interfaces between chains.
- C–D · 782 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- D–A · 416 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–A · 414 Ų buried · 3 hydrogen bonds · protein-nucleic
- D–B · 388 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–B · 365 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1YNW · Crystal Structure of Vitamin D Receptor and 9-cis Retinoic Acid Receptor DNA-Binding… · the same entry in another collection · chain C against C, TM-score 1.00
- P11473 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P11473) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P11473
- Every structure of UniProt P19793
- Elsewhere: RCSB PDB 1YNW · PDBe 1YNW · UniProt P11473 · UniProt P19793
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