MolNFT v1 · #111325 · protein
Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound
4YNK · Vitamin D3 RECEPTOR,VITAMIN D3 receptor: “Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound”. X-ray diffraction, 1 ligand (YW2), 2 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 4YNK
- Type
- protein
- Length
- 250 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 RECEPTOR,VITAMIN D3 receptor; Coactivator peptide drip from cdna FLJ50196…
- UniProt
- P13053
- Ligands
- YW2
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 RECEPTOR,VITAMIN D3 receptor | protein | 240 | 65% helix, 3% strand | P13053 |
| C | Coactivator peptide drip from cdna FLJ50196, highly similar to peroxisome proliferator-activated receptor-binding protein | protein | 10 | 70% helix, 0% strand | — |
Ligands and binding sites
- YW2 · (1R,3R,7E,17beta)-17-{(5S)-5-hydroxy-5-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-1-yl]penta-1,3-diyn-1-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
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 | 383 | 0.87 | 0.95 | 41 | YW2 |
| 2 | 63 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 532 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4YNK · Crystal structure of vitamin D receptor ligand binding domain complexed with a… · the same entry in another collection · chain A against A, TM-score 1.00
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 4YNK · PDBe 4YNK · UniProt P13053
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