MolNFT v1 · #82641 · protein
Crystal structures of rat vdr-lbd with W282R mutation
3VT8 · Vitamin D3 receptor: “Crystal structures of rat vdr-lbd with W282R mutation”. X-ray diffraction, 1 ligand (YI3), 3 pockets (best druggability 0.83). MolNFT v1 #82641 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VT8
- Type
- protein
- Length
- 244 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
- YI3
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 233 | 70% helix, 0% strand | P13053 |
| C | Coactivator peptide drip | protein | 11 | 55% helix, 0% strand | — |
Ligands and binding sites
- YI3 · (1R,3R,7E,9beta,17beta)-9-butyl-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-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 | 466 | 0.83 | 0.90 | 44 | YI3 |
| 2 | 73 | 0.36 | 0.77 | 15 | empty |
| 3 | 51 | 0.30 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–C · 577 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 3VT8 · PDBe 3VT8 · UniProt P13053
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