MolNFT v1 · #113922 · protein
Crystal structure of vdr-LBD/PARTIAL agonist complex: 22S-hexyl analogue
5AWJ · Vitamin D3 RECEPTOR,VITAMIN D3 receptor: “Crystal structure of vdr-LBD/PARTIAL agonist complex: 22S-hexyl analogue”. X-ray diffraction, 1 ligand (YSL), 2 pockets (best druggability 0.86). MolNFT v1 #113922 on GenesisL1: 3D…
- PDB
- 5AWJ
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 RECEPTOR,VITAMIN D3 receptor; Mediator of RNA polymerase II transcription…
- UniProt
- P13053, Q15648
- Ligands
- YSL
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 RECEPTOR,VITAMIN D3 receptor | protein | 240 | 68% helix, 3% strand | P13053 |
| C | Mediator of RNA polymerase II transcription subunit 1 | protein | 11 | 64% helix, 0% strand | Q15648 |
Ligands and binding sites
- YSL · (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)nonan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol · 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 | 410 | 0.86 | 0.94 | 40 | YSL |
| 2 | 78 | 0.36 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 560 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5AWJ · Crystal structure of VDR-LBD/partial agonist complex: 22S-hexyl analogue · 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 0.67
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 5AWJ · PDBe 5AWJ · UniProt P13053 · UniProt Q15648
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