New strategy to analyze structures of glycopeptide antibiotic-target complexes

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).

Ligands and binding sites

• RST · 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose · ligand · 2 copies · chains A, B, C
• MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, C, A
• BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B, C
• BXY · alpha-D-arabinofuranose · sugar · 2 copies · chains B, C
• RAM · alpha-L-rhamnopyranose · sugar · 2 copies · chains A, B, C
• GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
• SO4 · Sulfate ion · ion · 4 copies · chains A
• IPA · Isopropyl alcohol · additive · 3 copies · chains A

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.

Interfaces

3 interfaces between chains.

• A–B · 665 Ų buried · 13 hydrogen bonds · protein-protein
• B–C · 175 Ų buried · 6 hydrogen bonds · protein-protein
• A–C · 76 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified, 4 glycan, 2 covalent, 2 d-amino (nonstandard, glycosylation, covalent ligand, D-amino acid).

Compared structures

• 3RUM · New strategy to analyze structures of glycopeptide antibiotic-target complexes · the same entry in another collection · chain A against A, 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
• Every structure of UniProt P0AEX9
• Elsewhere: RCSB PDB 3RUM · PDBe 3RUM · UniProt P0AEX9