MolNFT v1 · #102214 · protein

Crystal structure of syg-1 D1, crystal form 1

4OF6 · Protein syg-1, isoform B: “Crystal structure of syg-1 D1, crystal form 1”. X-ray diffraction, 2 ligands (NAG, FUC), 2 pockets (best druggability 0.50). MolNFT v1 #102214 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OF6
Type: protein
Length: 223 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein syg-1, isoform B
UniProt: B1Q236
Ligands: NAG, FUC
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein syg-1, isoform B	protein	108	6% helix, 45% strand	B1Q236
B	Protein syg-1, isoform B	protein	115	8% helix, 41% strand	B1Q236

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
FUC · alpha-L-fucopyranose · sugar · 2 copies
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	165	0.50	0.77	26	EDO
2	92	0.44	0.79	24	empty

Interfaces

1 interface between chains.

A–B · 459 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4OF6 · Crystal Structure of SYG-1 D1, Crystal form 1 · 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 0.96

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 B1Q236
Elsewhere: RCSB PDB 4OF6 · PDBe 4OF6 · UniProt B1Q236

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