Research workbench
Crystal structure of rat vdr-lbd with 2-substituted-16-ene-22-thia- 1ALPHA,25-dihydroxy-26,27-dimethyl-19-norvitamin D3
Analyse Crystal structure of rat vdr-lbd with 2-substituted-16-ene-22-thia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VT6
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; Coactivator peptide drip
- UniProt
- P13053
- Ligands
- 5YI
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 240 | 66% helix, 3% strand | P13053 |
| C | Coactivator peptide drip | protein | 11 | 55% helix, 0% strand | — |
Ligands and binding sites
- 5YI · (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol · ligand · 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 | 353 | 0.87 | 0.96 | 42 | 5YI |
| 2 | 72 | 0.34 | 0.76 | 17 | empty |
| 3 | 50 | 0.30 | 0.76 | 9 | empty |
Interfaces
1 interface between chains.
- A–C · 566 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3VT6 · Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26… · 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
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
- Elsewhere: RCSB PDB 3VT6 · PDBe 3VT6 · UniProt P13053
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