Research workbench
Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator
Analyse Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LB4
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Retinoic acid receptor RXR-alpha; Nuclear receptor coactivator 2
- UniProt
- P19793, Q15596
- Ligands
- E8L
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.5 · 2 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor RXR-alpha | protein | 218 | 70% helix, 4% strand | P19793 |
| B | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
Ligands and binding sites
- E8L · 6-[ethyl-[3-(2-methoxyethoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.84 | 0.96 | 29 | E8L |
| 2 | 103 | 0.37 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 570 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6LB4 · Crystal structure of dimeric rxr-lbd complexed with net-3ME and TIF2 co-activator · 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 P19793
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 6LB4 · PDBe 6LB4 · UniProt P19793 · UniProt Q15596
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