3ib2: Difference between revisions

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-[[Image:3ib2.png|left|200px]]
-<!--
+==structure of the complex of C-terminal half (C-lobe) of bovine lactoferrin with alpha-methyl-4-(2-methylpropyl) benzene acetic acid==
-The line below this paragraph, containing "STRUCTURE_3ib2", creates the "Structure Box" on the page.
+<StructureSection load='3ib2' size='340' side='right'caption='[[3ib2]], [[Resolution|resolution]] 2.29&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3ib2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3hwq 3hwq], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fkx 3fkx] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qz1 2qz1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IB2 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.29&#8491;</td></tr>
--->
+<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>, <scene name='pdbligand=IBP:IBUPROFEN'>IBP</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3ib2|  PDB=3ib2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ib2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ib2 OCA], [https://pdbe.org/3ib2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ib2 RCSB], [https://www.ebi.ac.uk/pdbsum/3ib2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ib2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRFL_BOVIN TRFL_BOVIN] Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>   Lactotransferrin has antimicrobial activity. The most effective inhibitory activity was seen against E.coli and P.aeruginosa.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>   Lactoferricin B is an antimicrobial peptide. Inhibits the growth of Gram-negative and Gram-positive bacteria.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>   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.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>
+== 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/ib/3ib2_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3ib2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nonsteroidal antiinflammatory drugs (NSAIDs), due to their good efficacy in the treatment of pain, inflammation, and fever, are among the most prescribed class of medicines in the world. The main drawback of NSAIDs is that they induce gastric complications such as peptic ulceration and injury to the intestine. Four NSAIDs, indomethacin, diclofenac, aspirin, and ibuprofen were selected to induce gastropathy in mouse models. It was found that the addition of C-terminal half of bovine lactoferrin (C-lobe) reversed the NSAID-induced injuries to the extent of 47-70% whereas the coadministration of C-lobe prevented it significantly. The C-lobe was prepared proteolytically using serine proteases. The binding studies of C-lobe with NSAIDs showed that these compounds bind to C-lobe with affinities ranging from 2.6 to 4.8 x 10(-4) M. The complexes of C-lobe were prepared with the above four NSAIDs. All four complexes were crystallized and their detailed three-dimensional structures were determined using x-ray crystallographic method. The structures showed that all the four NSAID molecules bound to C-lobe at the newly identified ligand binding site in C-lobe that is formed involving two alpha-helices, alpha10 and alpha11. The ligand binding site is separated from the well known iron binding site by the longest and the most stable beta-strand, betaj, in the structure. Similar results were also obtained with the full length lactoferrin molecule. This novel, to our knowledge, binding site in C-lobe of lactoferrin shows a good complementarity for the acidic and lipophilic compounds such as NSAIDs. We believe this indicates that C-lobe of lactoferrin can be exploited for the prevention of NSAID-induced gastropathy.
-===structure of the complex of C-terminal half (C-lobe) of bovine lactoferrin with alpha-methyl-4-(2-methylpropyl) benzene acetic acid===
+The structural basis for the prevention of nonsteroidal antiinflammatory drug-induced gastrointestinal tract damage by the C-lobe of bovine colostrum lactoferrin.,Mir R, Singh N, Vikram G, Kumar RP, Sinha M, Bhushan A, Kaur P, Srinivasan A, Sharma S, Singh TP Biophys J. 2009 Dec 16;97(12):3178-86. PMID:20006955<ref>PMID:20006955</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ib2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20006955}}, adds the Publication Abstract to the page
+*[[Lactoferrin|Lactoferrin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20006955 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20006955}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3ib2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entries  and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qz1 2qz1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IB2 OCA].
-==Reference==
-<ref group="xtra">PMID:020006955</ref><references group="xtra"/>
 [[Category: Bos taurus]]
-[[Category: Kaur, P.]]
+[[Category: Large Structures]]
-[[Category: Kumar, R P.]]
+[[Category: Kaur P]]
-[[Category: Mir, R.]]
+[[Category: Kumar RP]]
-[[Category: Sharma, S.]]
+[[Category: Mir R]]
-[[Category: Singh, N.]]
+[[Category: Sharma S]]
-[[Category: Singh, T P.]]
+[[Category: Singh N]]
-[[Category: Sinha, M.]]
+[[Category: Singh TP]]
-[[Category: Vikram, G.]]
+[[Category: Sinha M]]
-[[Category: Antibiotic]]
+[[Category: Vikram G]]
-[[Category: Antimicrobial]]
-[[Category: C-lobe]]
-[[Category: Complex]]
-[[Category: Disulfide bond]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Ibuprofen]]
-[[Category: Ion transport]]
-[[Category: Iron]]
-[[Category: Iron transport]]
-[[Category: Metal binding protein]]
-[[Category: Metal-binding]]
-[[Category: Phosphoprotein]]
-[[Category: Protease]]
-[[Category: Secreted]]
-[[Category: Serine protease]]
-[[Category: Transport]]