Research workbench
Vitamin D receptor with a synthetic ligand ADRO1
Analyse Vitamin D receptor with a synthetic ligand ADRO1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XZF
- Type
- protein
- Length
- 247 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; Mediator of RNA polymerase II transcription subunit 1
- UniProt
- P13053, Q15648
- Ligands
- 8J0
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 237 | 68% helix, 3% strand | P13053 |
| C | Mediator of RNA polymerase II transcription subunit 1 | protein | 10 | 70% helix, 0% strand | Q15648 |
Ligands and binding sites
- 8J0 · (1R,3S,5Z)-5-[(2E)-2-[(1r,3as,7ar)-1-[(2R,6S)-6-(1-adamantyl)-6-oxidanyl-hex-4-yn-2-yl]-7A-methyl-2,3,3A, 5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol · ligand · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.86 | 0.95 | 41 | 8J0, FMT |
| 2 | 52 | 0.31 | 0.76 | 9 | empty |
| 3 | 53 | 0.26 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 534 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5XZF · Vitamin D receptor with a synthetic ligand ADRO1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.75
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 P13053
- Every structure of UniProt Q15648
- Elsewhere: RCSB PDB 5XZF · PDBe 5XZF · UniProt P13053 · UniProt Q15648
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