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X-ray crystal structure of the PYR1-pyrabactin a complex

Analyse X-ray crystal structure of the PYR1-pyrabactin a complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NJO
Type: protein
Length: 517 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Abscisic acid receptor PYR1
UniProt: O49686
Ligands: PYV, P2M, NA, SO4, CL
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Abscisic acid receptor PYR1	protein	169	29% helix, 37% strand	O49686
B	Abscisic acid receptor PYR1	protein	177	28% helix, 36% strand	O49686
C	Abscisic acid receptor PYR1	protein	171	27% helix, 37% strand	O49686

Ligands and binding sites

PYV · 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide · ligand · 2 copies · chains A, C
P2M · N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide · ligand · chains B
NA · Sodium ion · metal · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B, C
CL · Chloride ion · ion · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	292	0.81	0.92	32	PYV
2	300	0.81	0.92	34	P2M
3	301	0.77	0.88	34	PYV
4	228	0.49	0.75	29	CL
5	123	0.41	0.76	26	empty

Interfaces

2 interfaces between chains.

A–C · 915 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 754 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3NJO · X-ray crystal structure of the Pyr1-pyrabactin A complex · the same entry in another collection · chain A against A, TM-score 1.00
O49686 · AlphaFold monomer V2.0 prediction for abscisic acid receptor PYR1 (O49686) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O49686
Elsewhere: RCSB PDB 3NJO · PDBe 3NJO · UniProt O49686

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