Research workbench
Crystal structure of the retinoid X receptor alpha in complex with synthetic honokiol derivative 9 and a fragment of the TIF2 co- activator.
Analyse Crystal structure of the retinoid X receptor alpha in complex with synthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MKJ
- Type
- protein
- Length
- 220 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Lys-ile-leu-his-arg-leu-leu-gln-asp
- UniProt
- P19793
- Ligands
- 4CU
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 211 | 70% helix, 3% strand | P19793 |
| B | Lys-ile-leu-his-arg-leu-leu-gln-asp | protein | 9 | 78% helix, 0% strand | — |
Ligands and binding sites
- 4CU · (~{E})-3-[4-oxidanyl-3-(5-prop-2-enyl-2-propoxy-phenyl)phenyl]prop-2-enoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.84 | 0.96 | 29 | 4CU |
| 2 | 93 | 0.54 | 0.84 | 16 | empty |
| 3 | 112 | 0.41 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 486 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5MKJ · Crystal structure of the Retinoid X Receptor alpha in complex with synthetic honokiol… · 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
- Elsewhere: RCSB PDB 5MKJ · PDBe 5MKJ · UniProt P19793
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