Research workbench
Crystal structure of rarbeta lbd in complex with selective partial agonist BMS641 [3-chloro-4-[(E)-2-(5,5-dimethyl-8-phenyl-5,6- dihydronaphthalen-2-YL)ETHENYL]BENZOIC acid]
Analyse Crystal structure of rarbeta lbd in complex with selective partial agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JYI
- Type
- protein
- Length
- 497 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor beta; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- P10826, Q15788
- Ligands
- JYI
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinoic acid receptor beta | protein | 239 | 67% helix, 4% strand | P10826 |
| F | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 9 | 78% helix, 0% strand | Q15788 |
| G | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 70% helix, 0% strand | Q15788 |
Ligands and binding sites
- JYI · 3-chloro-4-[(E)-2-(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)ethenyl]benzoic acid · ligand · 2 copies · chains A, B
- FLC · Citrate anion · additive · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.84 | 0.96 | 34 | JYI |
| 2 | 262 | 0.83 | 0.94 | 37 | JYI |
| 3 | 540 | 0.71 | 0.80 | 49 | empty |
| 4 | 307 | 0.62 | 0.79 | 34 | empty |
| 5 | 113 | 0.47 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 968 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 545 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 528 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4JYI · Crystal structure of RARbeta LBD in complex with selective partial agonist BMS641… · the same entry in another collection · chain A against A, TM-score 1.00
- P10826 · AlphaFold monomer V2.0 prediction for retinoic acid receptor beta (P10826) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P10826
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 4JYI · PDBe 4JYI · UniProt P10826 · UniProt Q15788
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