1biy: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1biy.jpg|left|200px]]
- {{Structure
+==STRUCTURE OF DIFERRIC BUFFALO LACTOFERRIN==
-|PDB= 1biy |SIZE=350|CAPTION= <scene name='initialview01'>1biy</scene>, resolution 3.37&Aring;
+<StructureSection load='1biy' size='340' side='right'caption='[[1biy]], [[Resolution|resolution]] 3.37&Aring;' scene=''>
-|SITE= <scene name='pdbsite=FE1:Fe+Binding+Site+In+N-Lobe'>FE1</scene> and <scene name='pdbsite=FE2:Fe+Binding+Site+In+C-Lobe'>FE2</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>
+<table><tr><td colspan='2'>[[1biy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bubalus_bubalis Bubalus bubalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BIY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BIY FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.37&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1biy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1biy OCA], [https://pdbe.org/1biy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1biy RCSB], [https://www.ebi.ac.uk/pdbsum/1biy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1biy ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1biy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1biy OCA], [http://www.ebi.ac.uk/pdbsum/1biy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1biy RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/TRFL_BUBBU TRFL_BUBBU] Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate.  The lactotransferrin transferrin-like domain 1 functions as a serine protease of the peptidase S60 family that cuts arginine rich regions. This function contributes to the antimicrobial activity (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bi/1biy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1biy ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three-dimensional structure of diferric buffalo lactoferrin has been determined at 3.3 A resolution. The structure was solved by molecular replacement using the coordinates of diferric human lactoferrin as a search model and was refined by simulated annealing (X-PLOR). The final model comprises 5316 protein atoms for all 689 residues, two Fe(3+) and two CO(3)(2-) ions. The final R factor was 21.8% for 11 711 reflections in the resolution range 17.0-3.3 A. The folding of buffalo lactoferrin is essentially similar to that of the other members of the transferrin family. The significant differences are found in the dimensions of the binding cleft and the interlobe orientation. The interlobe interactions are predominantly hydrophobic in nature, thus facilitating the sliding of two lobes owing to external forces. The interdomain interactions are comparable in the N and C lobes.
-'''STRUCTURE OF DIFERRIC BUFFALO LACTOFERRIN'''
+Structure of buffalo lactoferrin at 3.3 A resolution at 277 K.,Karthikeyan S, Yadav S, Paramasivam M, Srinivasan A, Singh TP Acta Crystallogr D Biol Crystallogr. 2000 Jun;56(Pt 6):684-9. PMID:10818344<ref>PMID:10818344</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1biy" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The three-dimensional structure of diferric buffalo lactoferrin has been determined at 3.3 A resolution. The structure was solved by molecular replacement using the coordinates of diferric human lactoferrin as a search model and was refined by simulated annealing (X-PLOR). The final model comprises 5316 protein atoms for all 689 residues, two Fe(3+) and two CO(3)(2-) ions. The final R factor was 21.8% for 11 711 reflections in the resolution range 17.0-3.3 A. The folding of buffalo lactoferrin is essentially similar to that of the other members of the transferrin family. The significant differences are found in the dimensions of the binding cleft and the interlobe orientation. The interlobe interactions are predominantly hydrophobic in nature, thus facilitating the sliding of two lobes owing to external forces. The interdomain interactions are comparable in the N and C lobes.
+*[[Lactoferrin|Lactoferrin]]
+== References ==
-==About this Structure==
+<references/>
-BIY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bubalus_bubalis Bubalus bubalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BIY OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Structure of buffalo lactoferrin at 3.3 A resolution at 277 K., Karthikeyan S, Yadav S, Paramasivam M, Srinivasan A, Singh TP, Acta Crystallogr D Biol Crystallogr. 2000 Jun;56(Pt 6):684-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10818344 10818344]
 [[Category: Bubalus bubalis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Karthikeyan, S.]]
+[[Category: Karthikeyan S]]
-[[Category: Singh, T P.]]
+[[Category: Singh TP]]
-[[Category: Yadav, S.]]
+[[Category: Yadav S]]
-[[Category: antibacterial]]
-[[Category: iron binding protein]]
-[[Category: lactoferrin]]
-[[Category: structure]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:02:01 2008''