Crystal structure of group B streptococcus type III DP2 oligosaccharide bound to Fab nvs-1-19-5

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 55% strand (DSSP).

Ligands and binding sites

• 7GW · (2~{R},3~{R},4~{S},5~{S})-2-[bis(oxidanyl)methyl]-5-(hydroxymethyl)oxolane-3,4-diol · ligand · 2 copies · chains H, M
• GAL · beta-D-galactopyranose · sugar · 8 copies · chains H, L, M, N
• SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains H, L, M, N
• BGC · beta-D-glucopyranose · sugar · 4 copies · chains H, L, M, N
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H, L, M, N
• EDO · 1,2-ethanediol · additive · 13 copies · chains H, L, M, N

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• M–N · 2132 Ų buried · 17 hydrogen bonds · protein-protein
• H–L · 2034 Ų buried · 18 hydrogen bonds · protein-protein
• H–M · 466 Ų buried · 5 hydrogen bonds · protein-protein
• H–N · 17 Ų buried · 0 hydrogen bonds · protein-protein
• L–M · 16 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide (disulfide).

Compared structures

• 5M63 · Crystal structure of group B Streptococcus type III DP2 oligosaccharide bound to Fab… · the same entry in another collection · chain H against H, 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
• Elsewhere: RCSB PDB 5M63 · PDBe 5M63