1d1b: 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:1d1b.jpg|left|200px]]
-<!--
+==DICTYOSTELIUM MYOSIN S1DC (MOTOR DOMAIN FRAGMENT) COMPLEXED WITH O,P-DINITROPHENYL AMINOPROPYLDIPHOSPHATE BERYLLIUM TRIFLUORIDE.==
-The line below this paragraph, containing "STRUCTURE_1d1b", creates the "Structure Box" on the page.
+<StructureSection load='1d1b' size='340' side='right'caption='[[1d1b]], [[Resolution|resolution]] 2.00&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'>[[1d1b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D1B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D1B 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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAQ:O,P-DINITROPHENYL+AMINOPROPYLDIPHOSPHATE+BERYLLIUM+TRIFLUORIDE'>DAQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_1d1b|  PDB=1d1b  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d1b OCA], [https://pdbe.org/1d1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d1b RCSB], [https://www.ebi.ac.uk/pdbsum/1d1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d1b ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MYS2_DICDI MYS2_DICDI] Myosin is a protein that binds to actin and has ATPase activity that is activated by actin.
+== 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/d1/1d1b_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=1d1b ConSurf].
+<div style="clear:both"></div>
-'''DICTYOSTELIUM MYOSIN S1DC (MOTOR DOMAIN FRAGMENT) COMPLEXED WITH O,P-DINITROPHENYL AMINOPROPYLDIPHOSPHATE BERYLLIUM TRIFLUORIDE.'''
+==See Also==
+*[[Myosin 3D Structures|Myosin 3D Structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The three-dimensional structures of the truncated myosin head from Dictyostelium discoideum myosin II complexed with dinitrophenylaminoethyl-, dinitrophenylaminopropyl-, o-nitrophenylaminoethyl-, m-nitrophenylaminoethyl-, p-nitrophenylaminoethyl-, and o-nitrophenyl-N-methyl-aminoethyl-diphosphate.beryllium fluoride have been determined to better than 2.3-A resolution. The structure of the protein and nucleotide binding pocket in these complexes is very similar to that of S1dC.ADP.BeF(x) (Fisher, A. J., Smith, C. A., Thoden, J., Smith, R., Sutoh, K., Holden, H. M., and Rayment, I. (1995) Biochemistry 34, 8960-8972). The position of the triphosphate-like moiety is essentially identical in all complexes. Furthermore, the alkyl-amino group plays the same role as the ribose by linking the triphosphate to the adenine binding pocket; however, none of the phenyl groups lie in the same position as adenine in S1dC.MgADP.BeF(x), even though several of these nucleotide analogs are functionally equivalent to ATP. Rather the former location of adenine is occupied by water in the nanolog complexes, and the phenyl groups are organized in a manner that attempts to optimize their hydrogen bonding interactions with this constellation of solvent molecules. A comparison of the kinetic and structural properties of the nanologs relative to ATP suggests that the ability of a substrate to sustain tension and to generate movement correlates with a well defined interaction with the active site water structure observed in S1dC.MgADP.BeF(x).
-==About this Structure==
-D1B is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D1B OCA].
-==Reference==
-X-ray structures of the Dictyostelium discoideum myosin motor domain with six non-nucleotide analogs., Gulick AM, Bauer CB, Thoden JB, Pate E, Yount RG, Rayment I, J Biol Chem. 2000 Jan 7;275(1):398-408. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10617631 10617631]
 [[Category: Dictyostelium discoideum]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bauer, C B.]]
+[[Category: Bauer CB]]
-[[Category: Gulick, A M.]]
+[[Category: Gulick AM]]
-[[Category: Pate, E.]]
+[[Category: Pate E]]
-[[Category: Rayment, I.]]
+[[Category: Rayment I]]
-[[Category: Thoden, J B.]]
+[[Category: Thoden JB]]
-[[Category: Yount, R G.]]
+[[Category: Yount RG]]
-[[Category: Actin-binding]]
-[[Category: Motility]]
-[[Category: Motor domain]]
-[[Category: Myosin]]
-[[Category: Nanolog]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:20:18 2008''