MolNFT v1 · #137523 · protein

Aba-mimicking ligand AMF1ALPHA in complex with aba receptor PYL2 and PP2C HAB1

5VR7 · Abscisic acid receptor PYL2: “Aba-mimicking ligand AMF1ALPHA in complex with aba receptor PYL2 and PP2C HAB1”. X-ray diffraction, 2 ligands (A1F, MG), 4 pockets (best druggability 0.86). MolNFT v1 #137523 on GenesisL1: 3D structure…

PDB: 5VR7
Type: protein
Length: 486 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: A1F, MG
Pockets: 4 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Abscisic acid receptor PYL2	protein	176	28% helix, 38% strand	O80992
B	Protein phosphatase 2C 16 (EC 3.1.3.16)	protein	310	30% helix, 28% strand	Q9CAJ0

Ligands and binding sites

A1F · 1-(2-fluoro-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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	271	0.86	0.96	29	A1F
2	232	0.50	0.76	31	empty
3	79	0.30	0.73	18	empty
4	57	0.30	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 847 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5VR7 · ABA-mimicking ligand AMF1alpha 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 0.98
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 5VR7 · PDBe 5VR7 · UniProt O80992 · UniProt Q9CAJ0

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