Research workbench
Crystal structure of vdr-lbd complexed with 2-methylidene-19-nor-1A, 25-dihydroxyvitamin D3
Analyse Crystal structure of vdr-lbd complexed with 2-methylidene-19-nor-1A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B41
- Type
- protein
- Length
- 250 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
- YSV
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 239 | 67% helix, 3% strand | P13053 |
| C | Mediator of RNA polymerase II transcription subunit 1 | protein | 11 | 64% helix, 0% strand | Q15648 |
Ligands and binding sites
- YSV · (1R,3R)-5-(2-((1r,3as,7ar,e)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7A-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2-methylenecyclohexane-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 | 282 | 0.86 | 0.96 | 36 | YSV |
| 2 | 99 | 0.39 | 0.76 | 19 | empty |
| 3 | 53 | 0.32 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–C · 588 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5B41 · Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3 · 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 0.63
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 5B41 · PDBe 5B41 · UniProt P13053 · UniProt Q15648
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