Crystal structure of the polysaccharide deacetylase BC1974 from bacillus cereus in complex with N-hydroxynaphthalene-1-carboxamide

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Ligands and binding sites

• 8GK · ~{N}-oxidanylnaphthalene-1-carboxamide · ligand · 4 copies · chains A, D, B, C
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• NA · Sodium ion · metal · 2 copies · chains D
• EDO · 1,2-ethanediol · additive · chains B
• PGE · Triethylene glycol · additive · chains B, D

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

5 interfaces between chains.

• C–D · 516 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 504 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 467 Ų buried · 9 hydrogen bonds · protein-protein
• B–D · 439 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 343 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 5N1P · Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in… · the same entry in another collection · chain A against A, TM-score 1.00
• Q81EJ6 · AlphaFold monomer V2.0 prediction for peptidoglycan-N- acetylglucosamine deacetylase… · a predicted model of the same protein · 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 Q81EJ6
• Elsewhere: RCSB PDB 5N1P · PDBe 5N1P · UniProt Q81EJ6