Crystal structure of SCGAS2 in complex with compound 8

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 17% strand (DSSP).

Ligands and binding sites

• 9PW · [4-[[1-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]-1,2,3-triazol-4-yl]methoxymethyl]phenyl]-oxidanyl-oxidanylidene-azanium · ligand · chains C
• BGC · beta-D-glucopyranose · sugar · 3 copies · chains C
• SO4 · Sulfate ion · ion · 4 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 39 copies · chains A, B, C

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 993 Ų buried · 9 hydrogen bonds · protein-protein
• A–B · 806 Ų buried · 12 hydrogen bonds · protein-protein
• A–C · 469 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 disulfide (disulfide).

Compared structures

• Q06135 · AlphaFold monomer V2.0 prediction for 1,3-beta-glucanosyltransferase GAS2 (Q06135) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q06135
• Elsewhere: RCSB PDB 5OA2 · PDBe 5OA2 · UniProt Q06135