Research workbench
Crystal structure of rxralphalbd complexed with the agonist magnolol
Analyse Crystal structure of rxralphalbd complexed with the agonist magnolol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R5M
- Type
- protein
- Length
- 448 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
- MLO
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 215 | 66% helix, 4% strand | P19793 |
| B, D | Nuclear receptor coactivator 2 | protein | 10 | 80% helix, 0% strand | Q15596 |
| C | Retinoic acid receptor rxr-alpha | protein | 213 | 69% helix, 3% strand | P19793 |
Ligands and binding sites
- MLO · 5,5'-di(prop-2-en-1-yl)biphenyl-2,2'-diol · ligand · 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 | 192 | 0.83 | 0.97 | 27 | MLO |
| 2 | 251 | 0.81 | 0.92 | 38 | MLO |
| 3 | 797 | 0.73 | 0.78 | 64 | empty |
| 4 | 113 | 0.53 | 0.82 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1227 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 563 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 538 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3R5M · Crystal structure of RXRalphaLBD complexed with the agonist magnolol · 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 3R5M · PDBe 3R5M · UniProt P19793 · UniProt Q15596
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