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.


3c5m

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:44, 27 January 2022) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3c5m.jpg|left|200px]]
 
-
{{Structure
+
==Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR199==
-
|PDB= 3c5m |SIZE=350|CAPTION= <scene name='initialview01'>3c5m</scene>, resolution 2.60&Aring;
+
<StructureSection load='3c5m' size='340' side='right'caption='[[3c5m]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=AC1:Mn+Binding+Site+For+Residue+A+401'>AC1</scene>, <scene name='pdbsite=AC2:Mn+Binding+Site+For+Residue+B+401'>AC2</scene> and <scene name='pdbsite=AC3:Mn+Binding+Site+For+Residue+C+401'>AC3</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
+
<table><tr><td colspan='2'>[[3c5m]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibpa Vibpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C5M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C5M FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-
|GENE= VPA0088 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=223926 Vibrio parahaemolyticus RIMD 2210633])
+
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
|DOMAIN=
+
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VPA0088 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=223926 VIBPA])</td></tr>
-
|RELATEDENTRY=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c5m OCA], [https://pdbe.org/3c5m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c5m RCSB], [https://www.ebi.ac.uk/pdbsum/3c5m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c5m ProSAT], [https://www.topsan.org/Proteins/NESGC/3c5m TOPSAN]</span></td></tr>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c5m OCA], [http://www.ebi.ac.uk/pdbsum/3c5m PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3c5m RCSB]</span>
+
</table>
-
}}
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
'''Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR199'''
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
 
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c5/3c5m_consurf.spt"</scriptWhenChecked>
-
==About this Structure==
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
3C5M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_parahaemolyticus_rimd_2210633 Vibrio parahaemolyticus rimd 2210633]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C5M OCA].
+
<text>to colour the structure by Evolutionary Conservation</text>
-
[[Category: Single protein]]
+
</jmolCheckbox>
-
[[Category: Vibrio parahaemolyticus rimd 2210633]]
+
</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=3c5m ConSurf].
-
[[Category: Abashidze, M.]]
+
<div style="clear:both"></div>
-
[[Category: Acton, T B.]]
+
__TOC__
-
[[Category: Baran, M C.]]
+
</StructureSection>
-
[[Category: Forouhar, F.]]
+
[[Category: Large Structures]]
-
[[Category: Hunt, J F.]]
+
[[Category: Vibpa]]
-
[[Category: Janjua, H.]]
+
[[Category: Abashidze, M]]
-
[[Category: Mao, L.]]
+
[[Category: Acton, T B]]
-
[[Category: Montelione, G T.]]
+
[[Category: Baran, M C]]
-
[[Category: NESG, Northeast Structural Genomics Consortium.]]
+
[[Category: Forouhar, F]]
-
[[Category: Owens, L A.]]
+
[[Category: Hunt, J F]]
-
[[Category: Seetharaman, J.]]
+
[[Category: Janjua, H]]
-
[[Category: Tong, L.]]
+
[[Category: Mao, L]]
-
[[Category: Wang, D.]]
+
[[Category: Montelione, G T]]
-
[[Category: Xiao, R.]]
+
[[Category: Structural genomic]]
-
[[Category: 7 blade-shaped beta-propeller]]
+
[[Category: Owens, L A]]
-
[[Category: lyase]]
+
[[Category: Seetharaman, J]]
-
[[Category: nesg]]
+
[[Category: Tong, L]]
-
[[Category: northeast structural genomics consortium]]
+
[[Category: Wang, D]]
-
[[Category: protein structure initiative]]
+
[[Category: Xiao, R]]
-
[[Category: psi-2]]
+
[[Category: Blade-shaped beta-propeller]]
-
[[Category: structural genomic]]
+
[[Category: Lyase]]
-
 
+
[[Category: Nesg]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:30:46 2008''
+
[[Category: PSI, Protein structure initiative]]

Current revision

Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR199

PDB ID 3c5m

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/3c5m"
Personal tools