Research workbench
Vdr ligand binding domain in complex with 2-methylidene-19,24-dinor- 1ALPHA,25-dihydroxy VITAMIND3
Analyse Vdr ligand binding domain in complex with 2-methylidene-19,24-dinor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VRU
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; 13-meric peptide from mediator of RNA polymerase II transcription…
- UniProt
- P13053, Q15648
- Ligands
- YS3
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 238 | 66% helix, 3% strand | P13053 |
| C | 13-meric peptide from mediator of RNA polymerase II transcription subunit 1 | protein | 10 | 60% helix, 0% strand | Q15648 |
Ligands and binding sites
- YS3 · (1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-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 | 283 | 0.85 | 0.96 | 34 | YS3 |
| 2 | 75 | 0.33 | 0.75 | 16 | empty |
| 3 | 56 | 0.31 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–C · 544 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VRU · VDR ligand binding domain in complex with 2-Methylidene-19,24-dinor-1alpha,25-dihydroxy… · 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 0.76
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 3VRU · PDBe 3VRU · UniProt P13053 · UniProt Q15648
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