1W5U

GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)

1W5U の概要

• エントリーDOI: 10.2210/pdb1w5u/pdb
• 関連するPDBエントリー: 1AL4 1ALX 1ALZ 1AV2 1BDW 1C4D 1GMK 1GRM 1JNO 1JO3 1JO4 1KQE 1MAG 1MIC 1NG8 1NRM 1NRU 1NT5 1NT6 1TK2 1TKQ 2IZQ 2XDC 3L8L
• 関連するBIRD辞書のPRD_ID: PRD_000152
• 分子名称: GRAMICIDIN D, RUBIDIUM ION, CHLORIDE ION, ... (5 entities in total)
• 機能のキーワード: antibiotic, gramicidin, antifungal, antibacterial, membrane ion channel, linear gramicidin
• 由来する生物種: BACILLUS BREVIS; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 8984.51

構造登録者

Glowka, M.L.,Olczak, A.,Bojarska, J.,Szczesio, M.,Duax, W.L.,Burkhart, B.M.,Pangborn, W.A.,Langs, D.A.,Wawrzak, Z. (登録日: 2004-08-10, 公開日: 2005-09-15, 最終更新日: 2024-11-06)

主引用文献

Glowka, M.L.,Olczak, A.,Bojarska, J.,Szczesio, M.,Duax, W.L.,Burkhart, B.M.,Pangborn, W.A.,Langs, D.A.,Wawrzak, Z.
Structure of Gramicidin D-Rbcl Complex at Atomic Resolution from Low-Temperature Synchrotron Data: Interactions of Double-Stranded Gramicidin Channel Contents and Cations with Channel Wall
Acta Crystallogr.,Sect.D, 61:433-, 2005

PubMed Abstract: Gramicidin D (gD) is a naturally occurring ionophoric antibiotic that forms membrane channels specific for monovalent cations. The crystal structure of the RbCl complex of gD has been determined at 1.14 A resolution from low-temperature (100 K) synchrotron-radiation data with a final R of 16%. The structure was refined with anisotropic temperature factors for all non-H atoms and with partial occupancies for many of them. The asymmetric unit in the crystal contains four crystallographically independent molecules that form two right-handed antiparallel double-stranded dimers. There are seven distinct rubidium-binding sites in each dimeric channel. The occupancy factors of Rb cations are between 0.11 and 0.35 and the total ion contents of the two crystallographically independent channels are 1.59 and 1.22 ions, respectively. Although each channel is 'chemically symmetrical', the side-chain conformations, the distributions of rubidium cations and their binding sites in the two independent channels are not. Cations are 'coordinated' by delocalized pi-electrons of three to five carbonyl groups that together with peptide backbone chains form the gramicidin channel walls. The water:cation ratio in the channel interior is four or five:one, and five or six waters separate Rb cations during their passage through the channel.

PubMed: 15805598
DOI: 10.1107/S0907444905000399

実験手法

X-RAY DIFFRACTION (1.14 Å)