X-ray structure of neob from streptomyces fradiae in complex with plp and neomycin (as the external aldimine) at pH 9

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).

Ligands and binding sites

• OZY · (1R,2R,3S,4R,6S)-4,6-diamino-2-[(3-O-{2-amino-2,6-dideoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methyl)amino]-alpha-D-glucopyranosyl}-beta-D-ribofuranosyl)oxy]-3-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside · ligand · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains B
• EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3399 Ų buried · 57 hydrogen bonds · protein-protein

Compared structures

• 6CBM · x-ray structure of NeoB from streptomyces fradiae in complex with PLP and neomycin (as… · the same entry in another collection · chain A against A, TM-score 1.00
• Q53U08 · AlphaFold monomer V2.0 prediction for neamine transaminase neon (Q53U08) · 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 Q53U08
• Elsewhere: RCSB PDB 6CBM · PDBe 6CBM · UniProt Q53U08