Research workbench
A ligand M binding to fxr
Analyse A ligand M binding to fxr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YXL
- Type
- protein
- Length
- 445 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, E7EWM1
- Ligands
- NIW
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bile acid receptor | protein | 220 | 76% helix, 0% strand | Q96RI1 |
| B | Peptide from nuclear receptor coactivator 2 | protein | 7 | 71% helix, 0% strand | E7EWM1 |
| C | Bile acid receptor | protein | 210 | 75% helix, 0% strand | Q96RI1 |
| D | Peptide from nuclear receptor coactivator 2 | protein | 8 | 75% helix, 0% strand | E7EWM1 |
Ligands and binding sites
- NIW · 2-methoxyethyl propan-2-yl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.86 | 0.96 | 30 | NIW |
| 2 | 366 | 0.81 | 0.90 | 30 | NIW |
| 3 | 112 | 0.39 | 0.75 | 18 | empty |
| 4 | 131 | 0.39 | 0.74 | 22 | empty |
| 5 | 106 | 0.37 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 774 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 475 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 449 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5YXL · A ligand M binding to FXR · 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 E7EWM1
- Elsewhere: RCSB PDB 5YXL · PDBe 5YXL · UniProt Q96RI1 · UniProt E7EWM1
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