2ex6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:06, 6 November 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2ex6.png|left|200px]]
 
-
<!--
+
==Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with ampicillin==
-
The line below this paragraph, containing "STRUCTURE_2ex6", creates the "Structure Box" on the page.
+
<StructureSection load='2ex6' size='340' side='right'caption='[[2ex6]], [[Resolution|resolution]] 1.60&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'>[[2ex6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EX6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EX6 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]] 1.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AIX:(2R,4S)-2-[(1R)-1-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-OXOETHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC+ACID'>AIX</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-
{{STRUCTURE_2ex6| PDB=2ex6 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ex6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ex6 OCA], [https://pdbe.org/2ex6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ex6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ex6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ex6 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DACB_ECOLI DACB_ECOLI] Not involved in transpeptidation but exclusively catalyzes a DD-carboxypeptidase and DD-endopeptidase reaction.<ref>PMID:2046551</ref>
 +
== 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/ex/2ex6_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=2ex6 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The crystal structure of penicillin binding protein 4 (PBP4) from Escherichia coli, which has both DD-endopeptidase and DD-carboxypeptidase activity, is presented. PBP4 is one of 12 penicillin binding proteins in E. coli involved in the synthesis and maintenance of the cell wall. The model contains a penicillin binding domain similar to known structures, but includes a large insertion which folds into domains with unique folds. The structures of the protein covalently attached to five different antibiotics presented here show the active site residues are unmoved compared to the apoprotein, but nearby surface loops and helices are displaced in some cases. The altered geometry of conserved active site residues compared with those of other PBPs suggests a possible cause for the slow deacylation rate of PBP4.
-
===Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with ampicillin===
+
Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics.,Kishida H, Unzai S, Roper DI, Lloyd A, Park SY, Tame JR Biochemistry. 2006 Jan 24;45(3):783-92. PMID:16411754<ref>PMID:16411754</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2ex6" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_16411754}}, adds the Publication Abstract to the page
+
*[[Penicillin-binding protein|Penicillin-binding protein]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 16411754 is the PubMed ID number.
+
*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
-
-->
+
== References ==
-
{{ABSTRACT_PUBMED_16411754}}
+
<references/>
-
 
+
__TOC__
-
==About this Structure==
+
</StructureSection>
-
2EX6 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EX6 OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:16411754</ref><references group="xtra"/>
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Kishida, H.]]
+
[[Category: Large Structures]]
-
[[Category: Lloyd, A.]]
+
[[Category: Kishida H]]
-
[[Category: Park, S Y.]]
+
[[Category: Lloyd A]]
-
[[Category: Roper, D I.]]
+
[[Category: Park S-Y]]
-
[[Category: Tame, J R.H.]]
+
[[Category: Roper DI]]
-
[[Category: Unzai, S.]]
+
[[Category: Tame JRH]]
-
[[Category: Ampicillin]]
+
[[Category: Unzai S]]
-
[[Category: Cephem]]
+
-
[[Category: D-alanyl-d-alanine-carboxypeptidase]]
+
-
[[Category: D-alanyl-d-alanine-endopeptidase]]
+
-
[[Category: Penem]]
+
-
[[Category: Penicillin-binding protein]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:45:25 2009''
+

Current revision

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with ampicillin

PDB ID 2ex6

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/2ex6"
Personal tools