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Crystal structure of syg-1 D1, crystal form 2

Analyse Crystal structure of syg-1 D1, crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OF7
Type: protein
Length: 441 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein syg-1, isoform B
UniProt: B1Q236
Ligands: NAG, SO4
Pockets: 3 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein syg-1, isoform B	protein	109	6% helix, 46% strand	B1Q236
B	Protein syg-1, isoform B	protein	108	6% helix, 46% strand	B1Q236
C	Protein syg-1, isoform B	protein	114	5% helix, 45% strand	B1Q236
D	Protein syg-1, isoform B	protein	110	5% helix, 44% strand	B1Q236

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, D

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

Pockets

3 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	1056	0.81	0.83	107	empty
2	135	0.54	0.82	31	empty
3	95	0.43	0.79	30	empty

Interfaces

6 interfaces between chains.

A–C · 476 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 456 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 435 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 418 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 308 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4OF7 · Crystal Structure of SYG-1 D1, Crystal Form 2 · the same entry in another collection · chain D against D, TM-score 1.00
B1Q236 · AlphaFold monomer V2.0 prediction for synaptogenesis protein syg-1 (B1Q236) · a predicted model of the same protein · chain B 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 4OF7 · PDBe 4OF7 · UniProt B1Q236

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