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.


3kyf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:30, 20 March 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3kyf.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of P4397 complexed with c-di-GMP==
-
The line below this paragraph, containing "STRUCTURE_3kyf", creates the "Structure Box" on the page.
+
<StructureSection load='3kyf' size='340' side='right'caption='[[3kyf]], [[Resolution|resolution]] 2.10&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'>[[3kyf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida_KT2440 Pseudomonas putida KT2440]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KYF 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]] 2.1&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene></td></tr>
-
{{STRUCTURE_3kyf| PDB=3kyf | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyf OCA], [https://pdbe.org/3kyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kyf RCSB], [https://www.ebi.ac.uk/pdbsum/3kyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kyf ProSAT]</span></td></tr>
-
 
+
</table>
-
===Crystal structure of P4397 complexed with c-di-GMP===
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/YCGR_PSEPK YCGR_PSEPK] Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. Increasing levels of c-di-GMP lead to decreased motility (By similarity). Binds c-di-GMP with a dissociation constant of 165 nM. Binds 2 intercalated (c-di-GMP) dimers per subunit.
-
 
+
== Evolutionary Conservation ==
-
<!--
+
[[Image:Consurf_key_small.gif|200px|right]]
-
The line below this paragraph, {{ABSTRACT_PUBMED_20226196}}, adds the Publication Abstract to the page
+
Check<jmol>
-
(as it appears on PubMed at http://www.pubmed.gov), where 20226196 is the PubMed ID number.
+
<jmolCheckbox>
-
-->
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ky/3kyf_consurf.spt"</scriptWhenChecked>
-
{{ABSTRACT_PUBMED_20226196}}
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
3KYF is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYF OCA].
+
</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=3kyf ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
__TOC__
-
<ref group="xtra">PMID:20226196</ref><references group="xtra"/>
+
</StructureSection>
-
[[Category: Pseudomonas putida]]
+
[[Category: Large Structures]]
-
[[Category: Choi, B S.]]
+
[[Category: Pseudomonas putida KT2440]]
-
[[Category: Kim, H.]]
+
[[Category: Choi BS]]
-
[[Category: Ko, J.]]
+
[[Category: Kim H]]
-
[[Category: Ryu, K S.]]
+
[[Category: Ko J]]
-
[[Category: C-di-gmp]]
+
[[Category: Ryu KS]]
-
[[Category: Pilz domain]]
+
-
[[Category: Pp4397]]
+
-
[[Category: Unknown function]]
+
-
[[Category: Vca0042]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 14 09:35:08 2010''
+

Current revision

Crystal structure of P4397 complexed with c-di-GMP

PDB ID 3kyf

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/3kyf"
Personal tools