Research workbench
A moderator XD22 binding to bile acid receptor
Analyse A moderator XD22 binding to bile acid receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y49
- Type
- protein
- Length
- 472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bile acid receptor; Peptide from nuclear receptor coactivator 2
- UniProt
- Q96RI1, Q15596
- Ligands
- XD5
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bile acid receptor | protein | 224 | 74% helix, 0% strand | Q96RI1 |
| B | Bile acid receptor | protein | 227 | 75% helix, 0% strand | Q96RI1 |
| D | Peptide from nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
| E | Peptide from nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
Ligands and binding sites
- XD5 · [(1R,2S,4S)-2-bicyclo[2.2.1]heptanyl] 4-azanylbenzoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.82 | 0.98 | 24 | XD5 |
| 2 | 131 | 0.81 | 0.98 | 24 | XD5 |
| 3 | 53 | 0.56 | 0.90 | 13 | empty |
| 4 | 103 | 0.56 | 0.84 | 28 | empty |
| 5 | 154 | 0.54 | 0.80 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–D · 593 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 555 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 319 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5Y49 · A moderator XD22 binding to bile acid receptor · 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 Q96RI1
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 5Y49 · PDBe 5Y49 · UniProt Q96RI1 · UniProt Q15596
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