Research workbench
Crystal structure of rxr gamma lbd in complexes with palmitic acid and grip-1 peptide
Analyse Crystal structure of rxr gamma lbd in complexes with palmitic acid and grip-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A79
- Type
- protein
- Length
- 458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-gamma; Nuclear receptor coactivator 2
- UniProt
- P48443, Q15596
- Ligands
- PLM
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-gamma | protein | 215 | 71% helix, 3% strand | P48443 |
| B | Retinoic acid receptor rxr-gamma | protein | 217 | 69% helix, 3% strand | P48443 |
| C, D | Nuclear receptor coactivator 2 | protein | 13 | 62% helix, 0% strand | Q15596 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.83 | 0.93 | 40 | PLM |
| 2 | 292 | 0.80 | 0.90 | 37 | PLM |
| 3 | 392 | 0.63 | 0.78 | 29 | empty |
| 4 | 373 | 0.62 | 0.78 | 32 | empty |
| 5 | 52 | 0.58 | 0.91 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1172 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 571 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 568 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7A79 · Crystal structure of RXR gamma LBD in complexes with palmitic acid and GRIP-1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P48443 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr- gamma (P48443) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P48443
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 7A79 · PDBe 7A79 · UniProt P48443 · UniProt Q15596
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