This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1d1c

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:47, 7 February 2024) (edit) (undo)
 
(18 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1d1c.jpg|left|200px]]<br /><applet load="1d1c" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1d1c, resolution 2.3&Aring;" />
 
-
'''DICTYOSTELIUM MYOSIN S1DC (MOTOR DOMAIN FRAGMENT) COMPLEXED WITH N-METHYL-O-NITROPHENYL AMINOETHYLDIPHOSPHATE BERYLLIUM TRIFLUORIDE.'''<br />
 
-
==Overview==
+
==DICTYOSTELIUM MYOSIN S1DC (MOTOR DOMAIN FRAGMENT) COMPLEXED WITH N-METHYL-O-NITROPHENYL AMINOETHYLDIPHOSPHATE BERYLLIUM TRIFLUORIDE.==
-
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).
+
<StructureSection load='1d1c' size='340' side='right'caption='[[1d1c]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1d1c]] 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=1D1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D1C FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMQ:N-METHYL+O-NITROPHENYL+AMINOETHYLDIPHOSPHATE+BERYLLIUM+TRIFLUORIDE'>NMQ</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=1d1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d1c OCA], [https://pdbe.org/1d1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d1c RCSB], [https://www.ebi.ac.uk/pdbsum/1d1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d1c 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/d1/1d1c_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=1d1c ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1D1C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=NMQ:'>NMQ</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D1C OCA].
+
*[[Myosin 3D Structures|Myosin 3D Structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10617631 10617631]
+
[[Category: Dictyostelium discoideum]]
[[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: MG]]
+
-
[[Category: NMQ]]
+
-
[[Category: actin-binding]]
+
-
[[Category: motility]]
+
-
[[Category: motor domain]]
+
-
[[Category: myosin]]
+
-
[[Category: nanologs]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:11:52 2008''
+

Current revision

DICTYOSTELIUM MYOSIN S1DC (MOTOR DOMAIN FRAGMENT) COMPLEXED WITH N-METHYL-O-NITROPHENYL AMINOETHYLDIPHOSPHATE BERYLLIUM TRIFLUORIDE.

PDB ID 1d1c

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1d1c"
Personal tools