4ubp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (18:03, 20 September 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:4ubp.png|left|200px]]
 
-
<!--
+
==STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION==
-
The line below this paragraph, containing "STRUCTURE_4ubp", creates the "Structure Box" on the page.
+
<StructureSection load='4ubp' size='340' side='right'caption='[[4ubp]], [[Resolution|resolution]] 1.55&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'>[[4ubp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UBP 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]] 1.55&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=HAE:ACETOHYDROXAMIC+ACID'>HAE</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-
{{STRUCTURE_4ubp| PDB=4ubp | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ubp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubp OCA], [https://pdbe.org/4ubp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ubp RCSB], [https://www.ebi.ac.uk/pdbsum/4ubp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubp ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/URE3_SPOPA URE3_SPOPA]
 +
== 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/ub/4ubp_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=4ubp ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The structure of Bacillus pasteurii urease inhibited with acetohydroxamic acid was solved and refined anisotropically using synchrotron X-ray cryogenic diffraction data (1.55 A resolution, 99.5% completeness, data redundancy = 26, R-factor = 15.1%, PDB code 4UBP). The two Ni ions in the active site are separated by a distance of 3.53 A. The structure clearly shows the binding mode of the inhibitor anion, symmetrically bridging the two Ni ions in the active site through the hydroxamate oxygen and chelating one Ni ion through the carbonyl oxygen. The flexible flap flanking the active site cavity is in the open conformation. The possible implications of the results on structure-based molecular design of new urease inhibitors are discussed.
-
===STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION===
+
The complex of Bacillus pasteurii urease with acetohydroxamate anion from X-ray data at 1.55 A resolution.,Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S J Biol Inorg Chem. 2000 Feb;5(1):110-8. PMID:10766443<ref>PMID:10766443</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 4ubp" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_10766443}}, adds the Publication Abstract to the page
+
*[[Urease 3D structures|Urease 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 10766443 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_10766443}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
4UBP is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBP OCA].
+
-
 
+
-
==Reference==
+
-
The complex of Bacillus pasteurii urease with acetohydroxamate anion from X-ray data at 1.55 A resolution., Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S, J Biol Inorg Chem. 2000 Feb;5(1):110-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10766443 10766443]
+
-
[[Category: Protein complex]]
+
[[Category: Sporosarcina pasteurii]]
[[Category: Sporosarcina pasteurii]]
-
[[Category: Urease]]
+
[[Category: Benini S]]
-
[[Category: Benini, S.]]
+
[[Category: Ciurli S]]
-
[[Category: Ciurli, S.]]
+
[[Category: Mangani S]]
-
[[Category: Mangani, S.]]
+
[[Category: Rypniewski WR]]
-
[[Category: Rypniewski, W R.]]
+
[[Category: Wilson KS]]
-
[[Category: Wilson, K S.]]
+
-
[[Category: Acetohydroxamic acid]]
+
-
[[Category: Bacillus pasteurii]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Metalloenzyme]]
+
-
[[Category: Nickel]]
+
-
[[Category: Urease]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 17 13:11:17 2008''
+

Current revision

STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION

PDB ID 4ubp

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/4ubp"
Personal tools