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The 2.0 ångström resolution crystal structure of the rxralpha ligand binding domain tetramer in the presence of a non-activating retinoic acid isomer.
Analyse The 2.0 ångström resolution crystal structure of the rxralpha ligand binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G5Y
- Type
- protein
- Length
- 912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha
- UniProt
- P19793
- Ligands
- REA
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 228 | 64% helix, 3% strand | P19793 |
| B, D | Retinoic acid receptor rxr-alpha | protein | 229 | 72% helix, 2% strand | P19793 |
| C | Retinoic acid receptor rxr-alpha | protein | 226 | 68% helix, 2% strand | P19793 |
Ligands and binding sites
- REA · Retinoic acid · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.84 | 0.85 | 82 | REA |
| 2 | 722 | 0.84 | 0.87 | 78 | empty |
| 3 | 357 | 0.77 | 0.86 | 43 | REA |
| 4 | 190 | 0.64 | 0.84 | 23 | empty |
| 5 | 150 | 0.60 | 0.84 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1293 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1267 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1264 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1175 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1G5Y · The 2.0 ångström resolution crystal structure of the rxralpha ligand binding domain… · 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 1G5Y · PDBe 1G5Y · UniProt P19793
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