Research workbench
Complex structure of abscisic acid receptor PYL3 with (-)-aba
Analyse Complex structure of abscisic acid receptor PYL3 with (-)-aba in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JDA
- Type
- protein
- Length
- 695 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abscisic acid receptor PYL3
- UniProt
- Q9SSM7
- Ligands
- A9S
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Abscisic acid receptor PYL3 | protein | 177 | 27% helix, 37% strand | Q9SSM7 |
| B | Abscisic acid receptor PYL3 | protein | 171 | 29% helix, 36% strand | Q9SSM7 |
| C | Abscisic acid receptor PYL3 | protein | 173 | 29% helix, 36% strand | Q9SSM7 |
| D | Abscisic acid receptor PYL3 | protein | 174 | 26% helix, 34% strand | Q9SSM7 |
Ligands and binding sites
- A9S · (2Z,4E)-5-[(1R)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.83 | 0.94 | 31 | A9S |
| 2 | 428 | 0.81 | 0.89 | 59 | A9S |
| 3 | 492 | 0.79 | 0.86 | 58 | A9S |
| 4 | 418 | 0.79 | 0.87 | 49 | A9S |
| 5 | 615 | 0.77 | 0.83 | 78 | empty |
Interfaces
3 interfaces between chains.
- A–B · 920 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 898 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 496 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4JDA · Complex structure of abscisic acid receptor PYL3 with (-)-ABA · the same entry in another collection · chain D against D, TM-score 1.00
- Q9SSM7 · AlphaFold monomer V2.0 prediction for abscisic acid receptor PYL3 (Q9SSM7) · a predicted model of the same protein · chain B 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 Q9SSM7
- Elsewhere: RCSB PDB 4JDA · PDBe 4JDA · UniProt Q9SSM7
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