1gac
From Proteopedia
(New page: 200px<br /><applet load="1gac" size="450" color="white" frame="true" align="right" spinBox="true" caption="1gac" /> '''ASYMMETRIC HOMODIMER OF A82846B, A GLYCOPEPT...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1gac.gif|left|200px]]<br /><applet load="1gac" size=" | + | [[Image:1gac.gif|left|200px]]<br /><applet load="1gac" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1gac" /> | caption="1gac" /> | ||
'''ASYMMETRIC HOMODIMER OF A82846B, A GLYCOPEPTIDE ANTIBIOTIC, COMPLEXED WITH ITS CELL WALL PENTAPEPTIDE FRAGMENT, NMR, 80 MODELS'''<br /> | '''ASYMMETRIC HOMODIMER OF A82846B, A GLYCOPEPTIDE ANTIBIOTIC, COMPLEXED WITH ITS CELL WALL PENTAPEPTIDE FRAGMENT, NMR, 80 MODELS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Proton NMR assignments were determined for the asymmetric dimer complex of | + | Proton NMR assignments were determined for the asymmetric dimer complex of A82846B with the pentapeptide cell-wall fragment. A total of 683 experimental constraints, both distance and dihedral, were collected from NOESY and COSY data sets. From these constraints, a total of 80 structures were calculated using standard X-PLOR protocols. These structures were subsequently refined using the full CHARMm potential and the addition of water molecules in the calculation. The CHARMm structures occupied more conformational space than did the X-PLOR structures and were utilized for the structure analysis. From the structures, a unique set of interactions for the dALA-5 carboxylate pocket was observed, having backbone amides from residues 2 and 3 hydrogen bonding one carboxylate oxygen while amide 4 and the side chain amide from Asn-3 hydrogen bond the other oxygen. Also, near the N-terminal region of the ligand, the GGLU-2's carboxylate forms a hydrogen bond with the asymmetric disaccharide dyad, which helps to define the interactions seen for this part of the ligand. |
==About this Structure== | ==About this Structure== | ||
| - | 1GAC is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with VAX as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1GAC is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=VAX:'>VAX</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAC OCA]. |
==Reference== | ==Reference== | ||
Conformation of A82846B, a glycopeptide antibiotic, complexed with its cell wall fragment: an asymmetric homodimer determined using NMR spectroscopy., Prowse WG, Kline AD, Skelton MA, Loncharich RJ, Biochemistry. 1995 Jul 25;34(29):9632-44. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7626632 7626632] | Conformation of A82846B, a glycopeptide antibiotic, complexed with its cell wall fragment: an asymmetric homodimer determined using NMR spectroscopy., Prowse WG, Kline AD, Skelton MA, Loncharich RJ, Biochemistry. 1995 Jul 25;34(29):9632-44. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7626632 7626632] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Kline, A | + | [[Category: Kline, A D.]] |
| - | [[Category: Loncharich, R | + | [[Category: Loncharich, R J.]] |
| - | [[Category: Prowse, W | + | [[Category: Prowse, W G.]] |
| - | [[Category: Skelton, M | + | [[Category: Skelton, M A.]] |
[[Category: VAX]] | [[Category: VAX]] | ||
[[Category: antibiotic]] | [[Category: antibiotic]] | ||
| Line 22: | Line 22: | ||
[[Category: peptide]] | [[Category: peptide]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:47:55 2008'' |
Revision as of 10:47, 21 February 2008
|
ASYMMETRIC HOMODIMER OF A82846B, A GLYCOPEPTIDE ANTIBIOTIC, COMPLEXED WITH ITS CELL WALL PENTAPEPTIDE FRAGMENT, NMR, 80 MODELS
Overview
Proton NMR assignments were determined for the asymmetric dimer complex of A82846B with the pentapeptide cell-wall fragment. A total of 683 experimental constraints, both distance and dihedral, were collected from NOESY and COSY data sets. From these constraints, a total of 80 structures were calculated using standard X-PLOR protocols. These structures were subsequently refined using the full CHARMm potential and the addition of water molecules in the calculation. The CHARMm structures occupied more conformational space than did the X-PLOR structures and were utilized for the structure analysis. From the structures, a unique set of interactions for the dALA-5 carboxylate pocket was observed, having backbone amides from residues 2 and 3 hydrogen bonding one carboxylate oxygen while amide 4 and the side chain amide from Asn-3 hydrogen bond the other oxygen. Also, near the N-terminal region of the ligand, the GGLU-2's carboxylate forms a hydrogen bond with the asymmetric disaccharide dyad, which helps to define the interactions seen for this part of the ligand.
About this Structure
1GAC is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Conformation of A82846B, a glycopeptide antibiotic, complexed with its cell wall fragment: an asymmetric homodimer determined using NMR spectroscopy., Prowse WG, Kline AD, Skelton MA, Loncharich RJ, Biochemistry. 1995 Jul 25;34(29):9632-44. PMID:7626632
Page seeded by OCA on Thu Feb 21 12:47:55 2008
