Research workbench
Crystal structure of rat vdr ligand binding domain in complex with novel nonsecosteroidal ligands
Analyse Crystal structure of rat vdr ligand binding domain in complex with novel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W0J
- Type
- protein
- Length
- 253 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
- T08
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 242 | 65% helix, 3% strand | P13053 |
| C | Mediator of RNA polymerase II transcription subunit 1 | protein | 11 | 64% helix, 0% strand | Q15648 |
Ligands and binding sites
- T08 · (2S)-3-{4-[2-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)propan-2-yl]-2-methylphenoxy}propane-1,2-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 | 309 | 0.86 | 0.96 | 35 | T08 |
| 2 | 59 | 0.32 | 0.76 | 18 | empty |
| 3 | 56 | 0.31 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–C · 531 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3W0J · Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal… · 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 0.68
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 3W0J · PDBe 3W0J · UniProt P13053 · UniProt Q15648
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