1i3g

From Proteopedia

(Difference between revisions)

Revision as of 09:32, 10 January 2018

CRYSTAL STRUCTURE OF AN AMPICILLIN SINGLE CHAIN FV, FORM 1, FREE

Structural highlights

1i3g is a 2 chain structure with sequence from Lk3 transgenic mice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1h8s, 1h8o, 1h8n
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Single-chain Fv (scFv) antibody libraries were constructed from mice immunized with an ampicillin-bovine serum albumin conjugate. Several antibodies with specificity for intact ampicillin were selected by phage display and characterized. The antibody scFv fragment aL2 binds to intact ampicillin and shows no detectable cross-reactivity with hydrolyzed ampicillin. We determined the X-ray structures of two crystal forms of w.t. aL2, which differ mainly in the side-chain conformation of Trp H109 (according to a new consensus nomenclature Kabat residue number H95) in the extremely short (three residues) CDR H3 and the presence or absence of a well-resolved molecule of 2-methyl-pentane-2,4-diol in the bottom of the binding pocket. Attempts to co-crystallize aL2 with its antigen or to diffuse ampicillin into the wild-type aL2 crystals were unsuccessful, since crystal contacts obstruct the binding pocket. However, a mutant with two point mutations near the N terminus (Gln H6 replaced by Glu and Ala H10 (Kabat H9) replaced by Gly) crystallized in a form compatible with antigen-binding. Although the mutations affect the conformation of framework I, the conformations of the binding pocket of the uncomplexed wild-type aL2 and of the mutant complex were almost identical. The structure explains the specificity of the antibody for intact ampicillin and the degree of cross-reactivity of aL2 with a wide variety of ampicillin analogs. This antibody system will be very useful as a diagnostic reagent for antibiotics use and abuse, as a model for the effect of expression of antibiotic binding molecules in Escherichia coli, and for directed evolution towards high antibiotic resistance.

Selection, characterization and x-ray structure of anti-ampicillin single-chain Fv fragments from phage-displayed murine antibody libraries.,Burmester J, Spinelli S, Pugliese L, Krebber A, Honegger A, Jung S, Schimmele B, Cambillau C, Pluckthun A J Mol Biol. 2001 Jun 8;309(3):671-85. PMID:11397088^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Burmester J, Spinelli S, Pugliese L, Krebber A, Honegger A, Jung S, Schimmele B, Cambillau C, Pluckthun A. Selection, characterization and x-ray structure of anti-ampicillin single-chain Fv fragments from phage-displayed murine antibody libraries. J Mol Biol. 2001 Jun 8;309(3):671-85. PMID:11397088 doi:10.1006/jmbi.2001.4663

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1i3g"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF AN AMPICILLIN SINGLE CHAIN FV, FORM 1, FREE==
 <StructureSection load='1i3g' size='340' side='right' caption='[[1i3g]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1h8s|1h8s]], [[1h8o|1h8o]], [[1h8n|1h8n]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1i3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3g OCA], [http://pdbe.org/1i3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1i3g RCSB], [http://www.ebi.ac.uk/pdbsum/1i3g PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1i3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3g OCA], [http://pdbe.org/1i3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1i3g RCSB], [http://www.ebi.ac.uk/pdbsum/1i3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1i3g ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 11: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/1i3g_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/1i3g_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 ==See Also==
-*[[Monoclonal Antibody|Monoclonal Antibody]]
+*[[3D structures of monoclonal antibody|3D structures of monoclonal antibody]]
 == References ==
 <references/>

1i3g

From Proteopedia

Revision as of 09:32, 10 January 2018

CRYSTAL STRUCTURE OF AN AMPICILLIN SINGLE CHAIN FV, FORM 1, FREE

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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