1dsr
From Proteopedia
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|PDB= 1dsr |SIZE=350|CAPTION= <scene name='initialview01'>1dsr</scene> | |PDB= 1dsr |SIZE=350|CAPTION= <scene name='initialview01'>1dsr</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=AFA:N-[7-METHYL-OCT-2,4-DIENOYL]ASPARAGINE'>AFA</scene>, <scene name='pdbligand=AHB:BETA-HYDROXYASPARAGINE'>AHB</scene>, <scene name='pdbligand=CHP:3-CHLORO-4-HYDROXYPHENYLGLYCINE'>CHP</scene>, <scene name='pdbligand=D4P:(2S)-AMINO(4-HYDROXYPHENYL)ACETIC+ACID'>D4P</scene>, <scene name='pdbligand=GHP:4-HYDROXYPHENYLGLYCINE'>GHP</scene>, <scene name='pdbligand=ORN:ORNITHINE'>ORN</scene>, <scene name='pdbligand=SHP:(4-HYDROXYMALTOSEPHENYL)GLYCINE'>SHP</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dsr OCA], [http://www.ebi.ac.uk/pdbsum/1dsr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dsr RCSB]</span> | ||
}} | }} | ||
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[[Category: ramoplanin]] | [[Category: ramoplanin]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:47:57 2008'' |
Revision as of 16:47, 30 March 2008
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| Ligands: | , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
PEPTIDE ANTIBIOTIC, NMR, 6 STRUCTURES
Overview
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.
About this Structure
1DSR is a Protein complex structure of sequences from Actinoplanes sp.. Full crystallographic information is available from OCA.
Reference
3D structure of ramoplanin: a potent inhibitor of bacterial cell wall synthesis., Kurz M, Guba W, Biochemistry. 1996 Sep 24;35(38):12570-5. PMID:8823194
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