MolNFT v1 · #137573 · protein
Aba-mimicking ligand AMF4 in complex with aba receptor PYL2 and PP2C HAB1
5VSR · Abscisic acid receptor PYL2: “Aba-mimicking ligand AMF4 in complex with aba receptor PYL2 and PP2C HAB1”. X-ray diffraction, 2 ligands (AF0, MG), 5 pockets (best druggability 0.86). MolNFT v1 #137573 on GenesisL1: 3D structure…
- PDB
- 5VSR
- Type
- protein
- Length
- 481 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
- AF0, MG
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Abscisic acid receptor PYL2 | protein | 175 | 29% helix, 41% strand | O80992 |
| B | Protein phosphatase 2C 16 (EC 3.1.3.16) | protein | 306 | 34% helix, 27% strand | Q9CAJ0 |
Ligands and binding sites
- AF0 · N-(2-oxo-1-propyl-1,2,3,4-tetrahydroquinolin-6-yl)-1-(2,3,5,6-tetrafluoro-4-methylphenyl)methanesulfonamide · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.86 | 0.96 | 30 | AF0 |
| 2 | 241 | 0.54 | 0.78 | 33 | MG |
| 3 | 136 | 0.42 | 0.75 | 22 | empty |
| 4 | 79 | 0.39 | 0.77 | 13 | empty |
| 5 | 57 | 0.31 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1106 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VSR · ABA-mimicking ligand AMF4 in complex with ABA receptor PYL2 and PP2C HAB1 · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.97
- 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 0.94
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 5VSR · PDBe 5VSR · UniProt O80992 · UniProt Q9CAJ0
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