MolNFT v1 · #127038 · protein
Crystal structure of the retinoid X receptor alpha in complex with synthetic honokiol derivative 4 and a fragment of the TIF2 co- activator.
5MKU · Retinoic acid receptor rxr-alpha: “Crystal structure of the retinoid X receptor alpha in complex with synthetic honokiol derivative 4 and a…”. X-ray diffraction, 1 ligand (J57), 2 pockets (best druggability 0.77). MolNFT v1 #127038…
- PDB
- 5MKU
- Type
- protein
- Length
- 219 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; His-lys-ile-leu-his-arg-leu-leu-gln-asp-ser
- UniProt
- P19793
- Ligands
- J57
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 208 | 72% helix, 2% strand | P19793 |
| B | His-lys-ile-leu-his-arg-leu-leu-gln-asp-ser | protein | 11 | 55% helix, 0% strand | — |
Ligands and binding sites
- J57 · (~{E})-3-[4-oxidanyl-3-(3-propan-2-ylphenyl) phenyl]prop-2-enoic acid · ligand · 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 | 237 | 0.77 | 0.90 | 36 | J57 |
| 2 | 98 | 0.39 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 553 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5MKU · 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 5MKU · PDBe 5MKU · UniProt P19793
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