MolNFT v1 · #141143 · protein
Fxr ligand binding domain
5YXJ · Bile acid receptor: “Fxr ligand binding domain”. X-ray diffraction, 1 ligand (93U), 8 pockets (best druggability 0.86). MolNFT v1 #141143 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YXJ
- Type
- protein
- Length
- 467 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
- 93U
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bile acid receptor | protein | 225 | 75% helix, 0% strand | Q96RI1 |
| B | Bile acid receptor | protein | 220 | 75% helix, 0% strand | Q96RI1 |
| C, D | Peptide from nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | E7EWM1 |
Ligands and binding sites
- 93U · 2-[benzyl(methyl)amino]ethyl methyl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate · ligand · 2 copies · chains A, B
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 | 275 | 0.86 | 0.96 | 32 | 93U |
| 2 | 308 | 0.84 | 0.94 | 34 | 93U |
| 3 | 73 | 0.41 | 0.79 | 14 | empty |
| 4 | 51 | 0.40 | 0.81 | 11 | empty |
| 5 | 123 | 0.39 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–D · 534 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 440 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5YXJ · FXR ligand binding domain · 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 5YXJ · PDBe 5YXJ · UniProt Q96RI1 · UniProt E7EWM1
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