Research workbench
A unique binding model of fxr lbd with feroline
Analyse A unique binding model of fxr lbd with feroline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ICK
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bile acid receptor; Nuclear receptor coactivator 2
- UniProt
- Q96RI1, Q15596
- Ligands
- FEZ
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bile acid receptor | protein | 229 | 74% helix, 0% strand | Q96RI1 |
| C | Nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 10 | 80% helix, 0% strand | Q15596 |
Ligands and binding sites
- FEZ · (1S,2S,3Z,5S,8Z)-5-hydroxy-5,9-dimethyl-2-(propan-2-yl)cyclodeca-3,8-dien-1-yl 4-hydroxybenzoate · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.86 | 0.94 | 39 | FEZ |
| 2 | 183 | 0.84 | 0.97 | 26 | FEZ |
| 3 | 145 | 0.42 | 0.75 | 24 | empty |
| 4 | 156 | 0.42 | 0.74 | 26 | empty |
| 5 | 149 | 0.41 | 0.74 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–C · 607 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 555 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 472 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5ICK · A unique binding model of FXR LBD with feroline · 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 5ICK · PDBe 5ICK · UniProt Q96RI1 · UniProt Q15596
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