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Crystal structure of rarbeta lbd in complex with lg 100754
Analyse Crystal structure of rarbeta lbd in complex with lg 100754 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SSQ
- Type
- protein
- Length
- 509 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
- 754
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor beta | protein | 239 | 68% helix, 4% strand | P10826 |
| B | Retinoic acid receptor beta | protein | 249 | 65% helix, 4% strand | P10826 |
| F | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 80% helix, 0% strand | Q15788 |
| G | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 64% helix, 0% strand | Q15788 |
Ligands and binding sites
- 754 · (2E,4E,6Z)-3-methyl-7-(5,5,8,8-tetramethyl-3-propoxy-5, 6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid · ligand · 2 copies · chains A, B
- FLC · Citrate anion · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.84 | 0.96 | 35 | 754 |
| 2 | 291 | 0.84 | 0.94 | 39 | 754 |
| 3 | 332 | 0.64 | 0.80 | 30 | empty |
| 4 | 392 | 0.64 | 0.78 | 33 | empty |
| 5 | 144 | 0.48 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1196 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 539 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 506 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 6SSQ · PDBe 6SSQ · UniProt P10826 · UniProt Q15788
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