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Crystal Structure of SYG-1 D1-D2, Glycosylated

Analyse Crystal Structure of SYG-1 D1-D2, Glycosylated in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OF3
Type: protein
Length: 460 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.5
Source: Caenorhabditis elegans
Molecule: Protein SYG-1, isoform b
UniProt: B1Q236
Ligands: NAG, FUC, BMA
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · resolution 2.5 · 2 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein SYG-1, isoform b	protein	227	6% helix, 50% strand	B1Q236
B	Protein SYG-1, isoform b	protein	233	5% helix, 48% strand	B1Q236

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
BMA · beta-D-mannopyranose · sugar

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

Pockets

4 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	298	0.62	0.80	43	empty
2	106	0.36	0.74	20	empty
3	77	0.36	0.76	17	empty
4	81	0.35	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 904 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

4OF3 · Crystal structure of syg-1 D1-D2, glycosylated · the same entry in another collection · chain A against A, TM-score 1.00
B1Q236 · AlphaFold monomer V2.0 prediction for synaptogenesis protein syg-1 (B1Q236) · 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 B1Q236
Elsewhere: RCSB PDB 4OF3 · PDBe 4OF3 · UniProt B1Q236

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