Research workbench
Aba-mimicking ligand AMF2ALPHA in complex with aba receptor PYL2 and PP2C HAB1
Analyse Aba-mimicking ligand AMF2ALPHA in complex with aba receptor PYL2 and PP2C HAB1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VS5
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abscisic acid receptor PYL2; Protein phosphatase 2C 16
- EC
- 3.1.3.16
- UniProt
- O80992, Q9CAJ0
- Ligands
- 9J7, MG
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Abscisic acid receptor PYL2 | protein | 176 | 27% helix, 39% strand | O80992 |
| B | Protein phosphatase 2C 16 (EC 3.1.3.16) | protein | 296 | 31% helix, 30% strand | Q9CAJ0 |
Ligands and binding sites
- 9J7 · 1-(2,3-difluoro-4-methylphenyl)-N-(2-oxo-1-propyl-1,2, 3,4-tetrahydroquinolin-6-yl)methanesulfonamide · ligand · chains A, B
- MG · Magnesium ion · metal · 2 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 | 281 | 0.85 | 0.96 | 28 | 9J7 |
| 2 | 255 | 0.52 | 0.76 | 31 | empty |
| 3 | 59 | 0.45 | 0.83 | 18 | empty |
| 4 | 102 | 0.34 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 875 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5VS5 · ABA-mimicking ligand AMF2alpha in complex with ABA receptor PYL2 and PP2C 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
- O80992 · AlphaFold monomer V2.0 prediction for abscisic acid receptor PYL2 (O80992) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O80992
- Every structure of UniProt Q9CAJ0
- Elsewhere: RCSB PDB 5VS5 · PDBe 5VS5 · UniProt O80992 · UniProt Q9CAJ0
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