1DSR

Peptide antibiotic, NMR, 6 structures

1DSR の概要

• エントリーDOI: 10.2210/pdb1dsr/pdb
• 関連するBIRD辞書のPRD_ID: PRD_000222 PRD_900111
• 分子名称: RAMOPLANIN A2, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose, (2Z,4E)-7-methylocta-2,4-dienoic acid (3 entities in total)
• 機能のキーワード: ramoplanin, antibiotic, inhibitor, glycolipodespsipeptide
• 由来する生物種: ACTINOPLANES SP.
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 2608.11

構造登録者

Kurz, M.,Guba, W. (登録日: 1996-07-05, 公開日: 1997-02-12, 最終更新日: 2023-11-15)

主引用文献

Kurz, M.,Guba, W.
3D Structure of Ramoplanin: A Potent Inhibitor of Bacterial Cell Wall Synthesis.
Biochemistry, 35:12570-, 1996

PubMed Abstract: The 3D structure of ramoplanin was studied by NMR spectroscopy in aqueous solution. A total of 320 interproton distances were determined from a NOESY spectrum and were used as restraints in distance geometry calculations. A structural refinement was carried out by molecular dynamics calculations in a solvent box. The structure of ramoplanin is characterized by two antiparallel beta-strands which are formed by the residues 2-7 and 10-14, respectively. The beta-strands are connected by six intramolecular hydrogen bonds and a reverse beta-turn which is formed by Thr8 and Phe9 (in positions i+1 and i+2, respectively). Residues 2 and 14 are connected by a loop consisting of Leu15, Ala16, Chp17, and the side chain of Asn2. Although residues 14-17 show the formation of a beta-turn, only the N-terminal end of the turn is directly connected to one of the beta-strands (Gly14), whereas the C-terminal end (Chp17) is linked via the side chain of Asn2. The 3D conformation of ramoplanin is also stabilized by a hydrophobic cluster of the aromatic sidechains of the residues 3, 9, and 17. This hydrophobic collapse leads to a U-shaped topology of the beta-shee: with the beta-turn at one end and the loop at the other end. The structure found for ramoplanin differs corsiderably from the published structure of ramoplanose which might be due to a smaller number of NOE distance restraints used in the previous study.

PubMed: 8823194
DOI: 10.1021/BI961017Q

実験手法

SOLUTION NMR