Crystal structure of GENB4 in complex with external aldimine of plp- sisomicin

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).

Ligands and binding sites

• YS7 · (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,3,4,6-tetradeoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-erythro-hexopyranoside · ligand · chains A, B
• SBV · (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,3,4,6-tetradeoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-beta-L-threo-hexopyranoside · ligand · chains A, B
• CL · Chloride ion · ion · 4 copies · chains A, B
• PG4 · Tetraethylene glycol · additive · 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, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 4381 Ų buried · 75 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 7LLD · Crystal structure of GenB4 in complex with external aldimine of PLP-sisomicin · 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 Q6QVT7
• Elsewhere: RCSB PDB 7LLD · PDBe 7LLD · UniProt Q6QVT7