Research workbench
crystal structure of CAR/RXR heterodimer bound with SRC1 peptide, fatty acid, and 5b-pregnane-3,20-dione.
Analyse crystal structure of CAR/RXR heterodimer bound with SRC1 peptide, fatty acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XV9
- Type
- protein
- Length
- 1,002 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Retinoic acid receptor RXR-alpha; Orphan nuclear receptor NR1I3; nuclear receptor…
- UniProt
- P19793, Q14994
- Ligands
- F15, CI2
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.7 · 5 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Retinoic acid receptor RXR-alpha | protein | 232 | 61% helix, 4% strand | P19793 |
| B, D | Orphan nuclear receptor NR1I3 | protein | 246 | 67% helix, 4% strand | Q14994 |
| E | nuclear receptor coactivator 1 isoform 1 | protein | 10 | 80% helix, 0% strand | — |
| F | nuclear receptor coactivator 1 isoform 1 | protein | 12 | 50% helix, 0% strand | — |
| G, H | nuclear receptor coactivator 1 isoform 1 | protein | 12 | 50% helix, 0% strand | — |
Ligands and binding sites
- F15 · Pentadecanoic acid · ligand · 2 copies · chains A, C
- CI2 · (5beta)-pregnane-3,20-dione · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.87 | 0.97 | 30 | empty |
| 2 | 269 | 0.87 | 0.97 | 28 | CI2 |
| 3 | 1070 | 0.87 | 0.88 | 118 | empty |
| 4 | 257 | 0.85 | 0.96 | 34 | F15 |
| 5 | 277 | 0.85 | 0.96 | 32 | F15 |
Interfaces
11 interfaces between chains.
- A–B · 1307 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1220 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 663 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 643 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 568 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1XV9 · Crystal structure of CAR/RXR heterodimer bound with SRC1 peptide, fatty acid, and… · the same entry in another collection · chain H against H, TM-score 1.00
- Q14994 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 1 group I member 3… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P19793 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr- alpha (P19793) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q14994
- Elsewhere: RCSB PDB 1XV9 · PDBe 1XV9 · UniProt P19793 · UniProt Q14994
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