MolNFT v1 · #72792 · protein

X-ray crystal structure of the PYL2-pyrabactin a complex

3NJ0 · Abscisic acid receptor PYL2: “X-ray crystal structure of the PYL2-pyrabactin a complex”. X-ray diffraction, 1 ligand (PYV), 5 pockets (best druggability 0.86). MolNFT v1 #72792 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3NJ0
Type: protein
Length: 533 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Abscisic acid receptor PYL2
UniProt: O80992
Ligands: PYV
Pockets: 5 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Abscisic acid receptor PYL2	protein	177	29% helix, 38% strand	O80992
B	Abscisic acid receptor PYL2	protein	179	28% helix, 36% strand	O80992
C	Abscisic acid receptor PYL2	protein	177	29% helix, 37% strand	O80992

Ligands and binding sites

PYV · 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide · ligand · 3 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, C
GOL · Glycerol · additive · chains C

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.86	0.87	62	PYV, PEG
2	353	0.76	0.86	29	PYV, PEG, GOL
3	136	0.39	0.73	25	empty
4	110	0.36	0.73	23	empty
5	51	0.24	0.73	14	empty

Interfaces

2 interfaces between chains.

A–B · 921 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 526 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3NJ0 · X-ray crystal structure of the PYL2-pyrabactin A complex · 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 0.96

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
Elsewhere: RCSB PDB 3NJ0 · PDBe 3NJ0 · UniProt O80992

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