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High-resolution structure of pyrabactin-bound PYL2

Analyse High-resolution structure of pyrabactin-bound PYL2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NS2
Type: protein
Length: 541 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: 7 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Abscisic acid receptor PYL2	protein	181	28% helix, 36% strand	O80992
B	Abscisic acid receptor PYL2	protein	179	29% helix, 38% strand	O80992

Ligands and binding sites

PYV · 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide · ligand · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 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	890	0.87	0.89	63	PYV
2	361	0.75	0.85	31	PYV
3	165	0.49	0.77	26	empty
4	152	0.46	0.76	32	empty
5	166	0.40	0.73	27	empty

Interfaces

2 interfaces between chains.

A–B · 932 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 538 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3NS2 · High-resolution structure of pyrabactin-bound PYL2 · 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 B 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 3NS2 · PDBe 3NS2 · UniProt O80992

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