Research workbench
Crystal structure of human retinoid X receptor alpha-ligand binding domain complex with (R)4-methyl 9CUAB30 and coactivator peptide grip- 1
Analyse Crystal structure of human retinoid X receptor alpha-ligand binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M8H
- Type
- protein
- Length
- 225 residues
- Chains
- 2
- 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
- R4M
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 214 | 67% helix, 3% strand | P19793 |
| B | Nuclear receptor coactivator 2 | protein | 11 | 64% helix, 0% strand | Q15596 |
Ligands and binding sites
- R4M · (2E,6Z,8E)-3,7-dimethyl-8-[(4R)-4-methyl-3,4-dihydronaphthalen-1(2H)-ylidene]octa-2,6-dienoic 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 | 228 | 0.84 | 0.96 | 37 | R4M |
| 2 | 160 | 0.41 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4M8H · CRYSTAL STRUCTURE OF HUMAN RETINOID X RECEPTOR ALPHA-LIGAND BINDING DOMAIN COMPLEX WITH… · 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 4M8H · PDBe 4M8H · UniProt P19793 · UniProt Q15596
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