1mdc: Difference between revisions

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-{{Seed}}
-[[Image:1mdc.png|left|200px]]
-<!--
+==CRYSTALLIZATION, STRUCTURE DETERMINATION AND LEAST-SQUARES REFINEMENT TO 1.75 ANGSTROMS RESOLUTION OF THE FATTY-ACID-BINDING PROTEIN ISOLATED FROM MANDUCA SEXTA L==
-The line below this paragraph, containing "STRUCTURE_1mdc", creates the "Structure Box" on the page.
+<StructureSection load='1mdc' size='340' side='right'caption='[[1mdc]], [[Resolution|resolution]] 1.75&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'>[[1mdc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Manduca_sexta Manduca sexta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MDC 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]] 1.75&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1mdc|  PDB=1mdc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mdc OCA], [https://pdbe.org/1mdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mdc RCSB], [https://www.ebi.ac.uk/pdbsum/1mdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mdc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FABP2_MANSE FABP2_MANSE] Binds fatty acids in a 1:1 molar ratio.
+== 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/md/1mdc_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=1mdc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The molecular structure of an insect fatty-acid-binding protein isolated from Manduca sexta L. has been determined and refined to a nominal resolution of 1.75 A. Crystals used in the investigation were grown from 1.6 M-ammonium sulfate solutions buffered at pH 4.5 with 50 mM-sodium succinate, and belonged to space group P2(1) with unit cell dimensions of a = 27.5 A, b = 71.0 A, c = 28.7 A and beta = 90.8 degrees. An electron density map, phased with four heavy-atom derivatives and calculated to 2.5 A resolution, allowed for complete tracing of the 131 amino acid residue polypeptide chain. Subsequent least-squares refinement of the model reduced the R-factor from 46.0% to 17.3% using all measured X-ray data from 30.0 A to 1.75 A. Approximately 92% of the amino acid residues fall into classical secondary structural elements including ten strands of anti-parallel beta-pleated sheet, two alpha-helices, one type I turn, three type II turns, four type II' turns and one type III turn. As in other fatty-acid-binding proteins, the overall molecular architecture of the insect molecule consists of ten strands of anti-parallel beta-pleated sheet forming two layers that are nearly orthogonal to one another. A helix-turn-helix motif at the N-terminal portion of the protein flanks one side of the up-and-down beta-barrel. The functional group of the fatty acid is within hydrogen-bonding distance of Gln39, Tyr129, Arg127 and a sulfate molecule, while the aliphatic portion of the ligand is surrounded by hydrophobic amino acid residues lining the beta-barrel. The binding of the carboxylic acid portion of the ligand is very similar to that observed in P2 myelin protein and the murine adipocyte lipid-binding protein, but the positioning of the hydrocarbon tail after approximately C6 is completely different.
-===CRYSTALLIZATION, STRUCTURE DETERMINATION AND LEAST-SQUARES REFINEMENT TO 1.75 ANGSTROMS RESOLUTION OF THE FATTY-ACID-BINDING PROTEIN ISOLATED FROM MANDUCA SEXTA L===
+Crystallization, structure determination and least-squares refinement to 1.75 A resolution of the fatty-acid-binding protein isolated from Manduca sexta L.,Benning MM, Smith AF, Wells MA, Holden HM J Mol Biol. 1992 Nov 5;228(1):208-19. PMID:1447782<ref>PMID:1447782</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1mdc" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_1447782}}, adds the Publication Abstract to the page
+*[[Fatty acid-binding protein 3D structures|Fatty acid-binding protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 1447782 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_1447782}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-MDC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Manduca_sexta Manduca sexta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MDC OCA].
-==Reference==
-Crystallization, structure determination and least-squares refinement to 1.75 A resolution of the fatty-acid-binding protein isolated from Manduca sexta L., Benning MM, Smith AF, Wells MA, Holden HM, J Mol Biol. 1992 Nov 5;228(1):208-19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1447782 1447782]
 [[Category: Manduca sexta]]
-[[Category: Single protein]]
+[[Category: Benning M]]
-[[Category: Benning, M.]]
+[[Category: Holden HM]]
-[[Category: Holden, H M.]]
-[[Category: Binding protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 23:43:51 2008''