Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno- configured cyclophellitol aziridine

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).

Ligands and binding sites

• JIW · beta-D-manno-configured cyclophellitol aziridine, reacted form · ligand · chains A
• JIT · beta-D-manno-configured cyclophellitol aziridine · ligand · chains B
• VKH · (1~{R},2~{R},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol · ligand · chains B
• NA · Sodium ion · metal · 3 copies · chains A, B
• CL · Chloride ion · ion · 14 copies · chains A, B
• BR · Bromide ion · ion · 10 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 32 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 777 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 7OP6 · Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured cyclophellitol… · 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 Q8AAK6
• Elsewhere: RCSB PDB 7OP6 · PDBe 7OP6 · UniProt Q8AAK6