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Monocot chimeric jacalin JAC1 from oryza sativa: dirigent domain with bound galactobiose

Analyse Monocot chimeric jacalin JAC1 from oryza sativa: dirigent domain with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7YWF
Type: protein
Length: 432 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dirigent protein
UniProt: Q306J3
Ligands: GAL, PO4
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dirigent protein	protein	138	2% helix, 54% strand	Q306J3
B	Dirigent protein	protein	152	2% helix, 60% strand	Q306J3
C	Dirigent protein	protein	142	2% helix, 61% strand	Q306J3

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C
PO4 · Phosphate ion · ion · chains B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	215	0.74	0.89	33	empty
2	68	0.33	0.76	17	empty

Interfaces

3 interfaces between chains.

B–C · 1515 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 950 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 903 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7YWF · Monocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain with bound galactobiose · the same entry in another collection · chain A against A, TM-score 1.00

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 Q306J3
Elsewhere: RCSB PDB 7YWF · PDBe 7YWF · UniProt Q306J3

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