Research workbench
Crystal structure of vdr-lbd complexed with 22S-butyl-25- hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3
Analyse Crystal structure of vdr-lbd complexed with 22S-butyl-25… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XPL
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; Nuclear receptor coactivator 2
- UniProt
- P13053, Q15596
- Ligands
- 8C9
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 237 | 68% helix, 3% strand | P13053 |
| C | Nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
Ligands and binding sites
- 8C9 · (4~{S})-4-[(1~{R})-1-[(1~{R},3~{A}~{S},4~{E}, 7~{A}~{R})-7~{A}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl) cyclohexylidene]ethylidene]-2,3,3~{A},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(4-hydroxyphenyl)octan-1-one · 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 | 601 | 0.82 | 0.87 | 61 | 8C9 |
| 2 | 56 | 0.35 | 0.78 | 11 | empty |
| 3 | 54 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–C · 572 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5XPL · Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26… · 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
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 5XPL · PDBe 5XPL · UniProt P13053 · UniProt Q15596
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