Research workbench
Pyrabactin-bound PYL1 structure in the open and close forms
Analyse Pyrabactin-bound PYL1 structure in the open and close forms in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NEG
- Type
- protein
- Length
- 359 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abscisic acid receptor PYL1
- EC
- 3.1.3.16
- UniProt
- Q8VZS8
- Ligands
- PYV, BR
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Abscisic acid receptor PYL1 (EC 3.1.3.16) | protein | 182 | 28% helix, 35% strand | Q8VZS8 |
| B | Abscisic acid receptor PYL1 (EC 3.1.3.16) | protein | 177 | 30% helix, 33% strand | Q8VZS8 |
Ligands and binding sites
- PYV · 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide · ligand · 2 copies · chains A, B
- BR · Bromide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.79 | 0.91 | 31 | PYV, BR |
| 2 | 318 | 0.78 | 0.89 | 38 | empty |
| 3 | 264 | 0.74 | 0.87 | 31 | PYV |
| 4 | 132 | 0.50 | 0.80 | 21 | empty |
| 5 | 91 | 0.34 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 851 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 Q8VZS8
- Elsewhere: RCSB PDB 3NEG · PDBe 3NEG · UniProt Q8VZS8
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