NMR structure of asymmetric homodimer of A82846B, a glycopeptide antibiotic, complexed with its cell wall pentapeptide fragment

Structure

solution nmr · 2 distinct chains · 0% helix, 17% strand (DSSP).

Ligands and binding sites

• RER · vancosamine · ligand · 4 copies · chains A, C, D, B
• BGC · beta-D-glucopyranose · sugar · 2 copies · chains B, C, D

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

Interfaces

5 interfaces between chains.

• B–D · 301 Ų buried · 8 hydrogen bonds · protein-protein
• A–C · 294 Ų buried · 10 hydrogen bonds · protein-protein
• C–D · 199 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
• B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified, 4 d-amino, 2 covalent, 2 glycan (nonstandard, D-amino acid, covalent ligand, glycosylation).

Compared structures

• 1GAC · NMR structure of asymmetric homodimer of a82846b, a glycopeptide antibiotic, complexed… · 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
• Elsewhere: RCSB PDB 1GAC · PDBe 1GAC