Research workbench
An engineered PYR1 mandipropamid receptor in complex with mandipropamid and HAB1
Analyse An engineered PYR1 mandipropamid receptor in complex with mandipropamid and HAB1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WVO
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abscisic acid receptor PYR1; Protein phosphatase 2C 16
- EC
- 3.1.3.16
- UniProt
- O49686, Q9CAJ0
- Ligands
- 3UZ, MG
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Abscisic acid receptor PYR1 | protein | 174 | 30% helix, 39% strand | O49686 |
| B | Protein phosphatase 2C 16 (EC 3.1.3.16) | protein | 296 | 32% helix, 30% strand | Q9CAJ0 |
Ligands and binding sites
- 3UZ · (2S)-2-(4-chlorophenyl)-N-{2-[3-methoxy-4-(prop-2-yn-1-yloxy)phenyl]ethyl}-2-(prop-2-yn-1-yloxy)ethanamide · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.86 | 0.96 | 45 | 3UZ |
| 2 | 263 | 0.55 | 0.77 | 32 | MG |
| 3 | 67 | 0.32 | 0.75 | 10 | empty |
| 4 | 66 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4WVO · An engineered PYR1 mandipropamid receptor in complex with mandipropamid and HAB1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9CAJ0 · AlphaFold monomer V2.0 prediction for protein phosphatase 2C 16 (Q9CAJ0) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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
- Every structure of UniProt Q9CAJ0
- Elsewhere: RCSB PDB 4WVO · PDBe 4WVO · UniProt O49686 · UniProt Q9CAJ0
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