1baf

From Proteopedia

(Difference between revisions)

Current revision

2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN

Structural highlights

1baf is a 2 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:
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

The crystal structure of the Fab fragment of the murine monoclonal anti-dinitrophenyl-spin-label antibody AN02 complexed with its hapten has been solved at 2.9 A resolution using a novel molecular replacement method. Prior to translation searches, a large number of the most likely rotation function solutions were subjected to a rigid body refinement against the linear correlation coefficient between intensities of observed and calculated structure factors. First, the overall orientation of the search model and then the orientations and positions of the four Fab domains (VH, VL, CH1 and CL) were refined. This procedure clearly identified the correct orientation of the search model. The refined search model was then subjected to translation searches which unambiguously determined the enantiomer and position in the unit cell of the crystal. The successful search model was refined 2.5 A crystal structure of the Fab fragment of HyHel-5 from which non-matching residues in the variable domains had been removed. HyHel-5 is a murine monoclonal antibody whose heavy and light chains are of the same subclass (gamma 1, kappa, respectively) as AN02. After molecular replacement the structure of the AN02 Fab has been refined using simulated annealing in combination with model building and conjugate gradient refinement to a current crystallographic R-factor of 19.5% for 12,129 unique reflections between 8.0 and 2.9 A. The root-mean-square (r.m.s.) deviation from ideal bond lengths is 0.014 A, and the r.m.s. deviation from ideal bond angles is 3.1 degrees. The electron density reveals the hapten sitting in a pocket formed by the loops of the complementarity determining region. The dinitrophenyl ring of the hapten is sandwiched between the indole rings of Trp96 of the heavy-chain and Trp91 of the light-chain. The positioning of the hapten and general features of the combining site are in good agreement with the results of earlier nuclear magnetic resonance experiments.

2.9 A resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten.,Brunger AT, Leahy DJ, Hynes TR, Fox RO J Mol Biol. 1991 Sep 5;221(1):239-56. PMID:1920408^[1]

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

References

↑ Brunger AT, Leahy DJ, Hynes TR, Fox RO. 2.9 A resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten. J Mol Biol. 1991 Sep 5;221(1):239-56. PMID:1920408

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/1baf"

@@ Line 1: / Line 1: @@
 ==2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN==
-<StructureSection load='1baf' size='340' side='right' caption='[[1baf]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='1baf' size='340' side='right'caption='[[1baf]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1baf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BAF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BAF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1baf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BAF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NPP:N-(2-AMINO-ETHYL)-4,6-DINITRO-N-(2,2,6,6-TETRAMETHYL-1-OXY-PIPERIDIN-4-YL)-BENZENE-1,3-DIAMINE'>NPP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</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=1baf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1baf OCA], [http://pdbe.org/1baf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1baf RCSB], [http://www.ebi.ac.uk/pdbsum/1baf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1baf ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NPP:N-(2-AMINO-ETHYL)-4,6-DINITRO-N-(2,2,6,6-TETRAMETHYL-1-OXY-PIPERIDIN-4-YL)-BENZENE-1,3-DIAMINE'>NPP</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1baf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1baf OCA], [https://pdbe.org/1baf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1baf RCSB], [https://www.ebi.ac.uk/pdbsum/1baf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1baf 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/ba/1baf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ba/1baf_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 28: / Line 29: @@
 ==See Also==
-*[[3D structures of monoclonal antibody|3D structures of monoclonal antibody]]
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Brunger, A T]]
+[[Category: Large Structures]]
-[[Category: Fox, R O]]
+[[Category: Mus musculus]]
-[[Category: Hynes, T R]]
+[[Category: Brunger AT]]
-[[Category: Leahy, D J]]
+[[Category: Fox RO]]
-[[Category: Immune system]]
+[[Category: Hynes TR]]
-[[Category: Immunoglobulin]]
+[[Category: Leahy DJ]]

1baf

From Proteopedia

Current revision

2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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