MolNFT v1 · #127014 · protein
Crystal structure of the retinoid X receptor alpha in complex with synthetic honokiol derivative 7 and a fragment of the TIF2 co- activator.
5MK4 · Retinoic acid receptor rxr-alpha: “Crystal structure of the retinoid X receptor alpha in complex with synthetic honokiol derivative 7 and a…”. X-ray diffraction, 2 ligands (I5W, CL), 4 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5MK4
- Type
- protein
- Length
- 450 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Nuclear receptor coactivator 2
- UniProt
- P19793, Q15596
- Ligands
- I5W, CL
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 214 | 71% helix, 3% strand | P19793 |
| B | Nuclear receptor coactivator 2 | protein | 10 | 50% helix, 0% strand | Q15596 |
| C | Retinoic acid receptor rxr-alpha | protein | 215 | 72% helix, 3% strand | P19793 |
| D | Nuclear receptor coactivator 2 | protein | 11 | 55% helix, 0% strand | Q15596 |
Ligands and binding sites
- I5W · (~{E})-3-[3-(2-methyl-5-phenyl-phenyl)-4-oxidanyl-phenyl]prop-2-enoic acid · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.84 | 0.96 | 38 | I5W |
| 2 | 213 | 0.82 | 0.95 | 36 | I5W |
| 3 | 300 | 0.64 | 0.80 | 32 | empty |
| 4 | 351 | 0.58 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1085 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 575 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 554 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5MK4 · 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
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 5MK4 · PDBe 5MK4 · UniProt P19793 · UniProt Q15596
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