Crystal structure of aminoglycoside acetyltransferase AAC(3)-iva, H154A mutant, in complex with gentamicin C1A

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).

Ligands and binding sites

• LLL · (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-diamino-3-((2R, 3R,6S)-3-amino-6-(aminomethyl)-tetrahydro-2H-pyran-2-yloxy)-2-hydroxycyclohexyloxy)-5-methyl-4-(methylamino)-tetrahydro-2H-pyran-3,5-diol · ligand · 6 copies · chains A, B, C, D, E, F
• ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
• EDO · 1,2-ethanediol · additive · 41 copies · chains A, B, C, F, D, E
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 12 copies · chains A, B, C, F, D, E
• GOL · Glycerol · additive · 5 copies · chains A, B, C, F, D
• PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 3 copies · chains B, C, D

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–D · 818 Ų buried · 11 hydrogen bonds · protein-protein
• B–C · 800 Ų buried · 12 hydrogen bonds · protein-protein
• D–E · 614 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 609 Ų buried · 10 hydrogen bonds · protein-protein
• C–F · 597 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 6MN5 · Crystal structure of aminoglycoside acetyltransferase AAC(3)-IVa, H154A mutant, in… · 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 Q306W4
• Elsewhere: RCSB PDB 6MN5 · PDBe 6MN5 · UniProt Q306W4