1W3M

Crystal structure of tsushimycin

1W3M の概要

• エントリーDOI: 10.2210/pdb1w3m/pdb
• 関連するBIRD辞書のPRD_ID: PRD_000487
• 分子名称: TSUSHIMYCIN, Delta-3isotetradecenoic acid, CALCIUM ION, ... (6 entities in total)
• 機能のキーワード: amphomycin, daptomycin, lipopetide, antibiotic, antibacterial
• 由来する生物種: ACTINOPLANES FRIULIENSIS
• タンパク質・核酸の鎖数: 12
• 化学式量合計: 18225.35

構造登録者

Bunkoczi, G.,Vertesy, L.,Sheldrick, G.M. (登録日: 2004-07-16, 公開日: 2005-07-27, 最終更新日: 2025-04-09)

主引用文献

Bunkoczi, G.,Vertesy, L.,Sheldrick, G.M.
Structure of the lipopeptide antibiotic tsushimycin.
Acta Crystallogr. D Biol. Crystallogr., 61:1160-1164, 2005

PubMed Abstract: The amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 A resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods. The antibiotic is comprised of a cyclodecapeptide core, an exocyclic amino acid and a fatty-acid residue. Its backbone adopts a saddle-like conformation that is stabilized by a Ca2+ ion bound within the peptide ring and accounts for the Ca2+-dependence of this antibiotic class. Additional Ca2+ ions link the antibiotic molecules to dimers that enclose an empty space resembling a binding cleft. The dimers possess a large hydrophobic surface capable of interacting with the bacterial cell membrane. The antibiotic daptomycin may exhibit a similar conformation, as the amino-acid sequence is conserved at positions involved in Ca2+ binding.

PubMed: 16041082
DOI: 10.1107/S0907444905017270

実験手法

X-RAY DIFFRACTION (1 Å)