Crystal structure of glycopeptide hexose oxidase DBV29 complexed with teicoplanin

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 21% strand (DSSP).

Ligands and binding sites

• T55 · 8-methylnonanoic acid · ligand · 6 copies · chains B, L, A, K, C, M, N, O, P
• N1L · 2-amino-2-deoxy-beta-D-glucopyranuronic acid · ligand · 6 copies · chains A, K, B, L, C, M, N, O, P
• FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, K, B, L, C, M, D
• MAN · alpha-D-mannopyranose · sugar · 8 copies · chains B, I, C, J, K, L, M, N, A, O, P
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, I, C, J, A, K, L, M, N, O, P
• CIT · Citric acid · additive · 5 copies · chains A, B, C, D, O

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

14 interfaces between chains.

• A–B · 1402 Ų buried · 13 hydrogen bonds · protein-protein
• C–M · 623 Ų buried · 9 hydrogen bonds · protein-protein
• A–K · 600 Ų buried · 9 hydrogen bonds · protein-protein
• B–L · 584 Ų buried · 8 hydrogen bonds · protein-protein
• A–C · 445 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 56 modified, 16 glycan, 8 cofactor, 6 covalent, 1 disulfide (nonstandard, glycosylation, flavinylation, covalent ligand, disulfide).

Compared structures

• 5AWV · Crystal structure of glycopeptide hexose oxidase DBV29 complexed with teicoplanin · the same entry in another collection · chain B against B, 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 Q7WZ62
• Elsewhere: RCSB PDB 5AWV · PDBe 5AWV · UniProt Q7WZ62