MolNFT v1 · #140626 · protein
Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist
5YGV: “Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist”. X-ray diffraction, 1 ligand (8V6), 3 pockets (best druggability 0.85). MolNFT v1 #140626 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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