Research workbench
Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist
Analyse Crystal structure of the abscisic acid receptor PYR1 in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YGV
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abscisic acid receptor PYR1
- UniProt
- O49686
- Ligands
- 8V6
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Abscisic acid receptor PYR1 | protein | 168 | 29% helix, 36% strand | O49686 |
| B | Abscisic acid receptor PYR1 | protein | 172 | 28% helix, 35% strand | O49686 |
Ligands and binding sites
- 8V6 · (2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.85 | 0.94 | 37 | 8V6 |
| 2 | 296 | 0.80 | 0.90 | 31 | 8V6 |
| 3 | 53 | 0.28 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 623 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5YGV · Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist · the same entry in another collection · chain A against A, TM-score 1.00
- O49686 · AlphaFold monomer V2.0 prediction for abscisic acid receptor PYR1 (O49686) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O49686
- Elsewhere: RCSB PDB 5YGV · PDBe 5YGV · UniProt O49686
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