MolNFT v1 · #82341 · protein
Vitamin D receptor complex with a carborane compound
3VJS · Vitamin D3 receptor: “Vitamin D receptor complex with a carborane compound”. X-ray diffraction, 1 ligand (10S), 2 pockets (best druggability 0.87). MolNFT v1 #82341 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VJS
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; Peptide from mediator of RNA polymerase II transcription subunit 1
- UniProt
- P13053, Q15648
- Ligands
- 10S
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 239 | 68% helix, 3% strand | P13053 |
| C | Peptide from mediator of RNA polymerase II transcription subunit 1 | protein | 10 | 70% helix, 0% strand | Q15648 |
Ligands and binding sites
- 10S · 1-(2-[(S)-2,4-Dihydroxybutoxy]ethyl)-12-(5-ethyl-5-hydroxyheptyl)-1,12-dicarba-closo-dodecaborane · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.87 | 0.96 | 41 | 10S |
| 2 | 61 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 532 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3VJS · Vitamin D receptor complex with a carborane compound · the same entry in another collection · chain A against A, TM-score 1.00
- P13053 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P13053) · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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 0.77
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 3VJS · PDBe 3VJS · UniProt P13053 · UniProt Q15648
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