X-ray structure of GENB1 from micromonospora echinospora in complex with neamine and plp (as the external aldimine)

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).

Ligands and binding sites

• DOW · (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2-amino-2,6-dideoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-glucopyranoside · ligand · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 2 copies · chains C, D, B
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, B, D
• MPO · 3[N-morpholino]propane sulfonic acid · additive · 3 copies · chains A, B, C, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• C–D · 3556 Ų buried · 58 hydrogen bonds · protein-protein
• A–B · 3534 Ų buried · 60 hydrogen bonds · protein-protein
• B–D · 520 Ų buried · 11 hydrogen bonds · protein-protein
• A–C · 516 Ų buried · 11 hydrogen bonds · protein-protein
• B–C · 165 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 6CBO · X-ray structure of GenB1 from micromonospora echinospora in complex with neamine and PLP… · 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 Q70KD9
• Elsewhere: RCSB PDB 6CBO · PDBe 6CBO · UniProt Q70KD9