1fvm

Complex of vancomycin with DI-acetyl-LYS-D-ALA-D-ALA

spinqualitylabelsall models 1fvm, resolution 1.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1fvm is a 12 chain structure with sequence from Amycolatopsis orientalis. The December 2015 RCSB PDB Molecule of the Month feature on Vancomycin by David Goodsell is 10.2210/rcsb_pdb/mom_2015_12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.8Å Ligands: 3FG, BGC, DAL, DLS, GHP, MLU, OMY, OMZ, PRD_000204, RER Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed The crystal structures of three vancomycin complexes with two vancomycin-sensitive cell-wall precursor analogs (diacetyl-Lys-D-Ala-D-Ala and acetyl-D-Ala-D-Ala) and a vancomycin-resistant cell-wall precursor analog (diacetyl-Lys-D-Ala-D-lactate) were determined at atomic resolutions of 1.80 A, 1.07 A, and 0.93 A, respectively. These structures not only reconfirm the "back-to-back" dimerization of vancomycin monomers and the ligand-binding scheme proposed by previous experiments but also show important structural features of strategies for the generation of new glycopeptide antibiotics. These structural features involve a water-mediated antibiotic-ligand interaction and supramolecular structures such as "side-by-side" arranged dimer-to-dimer structures, in addition to ligand-mediated and "face-to-face" arranged dimer-to-dimer structures. In the diacetyl-Lys-D-Ala-D-lactate complex, the interatomic O...O distance between the carbonyl oxygen of the fourth residue of the antibiotic backbone and the ester oxygen of the D-lactate moiety of the ligand is clearly longer than the corresponding N-H...O hydrogen-bonding distance observed in the two other complexes due to electrostatic repulsion. In addition, two neighboring hydrogen bonds are concomitantly lengthened. These observations provide, at least in part, a molecular basis for the reduced antibacterial activity of vancomycin toward vancomycin-resistant bacteria with cell-wall precursors terminating in -D-Ala-D-lactate. Crystal structures of the complexes between vancomycin and cell-wall precursor analogs.,Nitanai Y, Kikuchi T, Kakoi K, Hanamaki S, Fujisawa I, Aoki K J Mol Biol. 2009 Feb 6;385(5):1422-32. Epub 2008 Oct 19. PMID:18976660 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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