Research workbench
Crystal structure of pyrabactin-bound abscisic acid receptor PYL1 in complex with type 2C protein phosphatase ABI1
Analyse Crystal structure of pyrabactin-bound abscisic acid receptor PYL1 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NMN
- Type
- protein
- Length
- 886 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abscisic acid receptor PYL1; Protein phosphatase 2C 56
- EC
- 3.1.3.16
- UniProt
- Q8VZS8, P49597
- Ligands
- PYV, MG
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Abscisic acid receptor PYL1 | protein | 168 | 29% helix, 35% strand | Q8VZS8 |
| B | Protein phosphatase 2C 56 (EC 3.1.3.16) | protein | 271 | 34% helix, 28% strand | P49597 |
| C | Abscisic acid receptor PYL1 | protein | 171 | 27% helix, 35% strand | Q8VZS8 |
| D | Protein phosphatase 2C 56 (EC 3.1.3.16) | protein | 276 | 34% helix, 29% strand | P49597 |
Ligands and binding sites
- PYV · 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.85 | 0.97 | 28 | PYV |
| 2 | 226 | 0.85 | 0.97 | 28 | PYV |
| 3 | 1068 | 0.77 | 0.79 | 74 | empty |
| 4 | 231 | 0.58 | 0.80 | 36 | empty |
| 5 | 292 | 0.58 | 0.78 | 40 | MG |
Interfaces
3 interfaces between chains.
- A–B · 914 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 882 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 555 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3NMN · Crystal structure of pyrabactin-bound abscisic acid receptor PYL1 in complex with type 2C… · the same entry in another collection · chain D against D, TM-score 1.00
- P49597 · AlphaFold monomer V2.0 prediction for protein phosphatase 2C 56 (P49597) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q8VZS8 · AlphaFold monomer V2.0 prediction for abscisic acid receptor PYL1 (Q8VZS8) · a predicted model of the same protein · chain C against A, TM-score 0.95
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
- Every structure of UniProt P49597
- Elsewhere: RCSB PDB 3NMN · PDBe 3NMN · UniProt Q8VZS8 · UniProt P49597
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