5jc6 - Revision history

OCA at 10:58, 6 September 2023

2023-09-06T10:58:37Z

←Older revision		Revision as of 10:58, 6 September 2023
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	==Carboxypeptidase B with 2-nd zinc and acetate ion==		==Carboxypeptidase B with 2-nd zinc and acetate ion==
-	<StructureSection load='5jc6' size='340' side='right' caption='[[5jc6]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5jc6' size='340' side='right'caption='[[5jc6]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jc6]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pig Pig~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JC6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jc6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JC6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'>ACT</scene~~>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CPB1, CPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9823 PIG])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Carboxypeptidase_B Carboxypeptidase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.2 3.4.17.2]~~ </~~span~~></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=5jc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc6 OCA], [https://pdbe.org/5jc6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jc6 RCSB], [https://www.ebi.ac.uk/pdbsum/5jc6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jc6 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5jc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc6 OCA], [~~http~~://pdbe.org/5jc6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jc6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jc6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jc6 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CBPB1_PIG CBPB1_PIG]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Carboxypeptidase\|Carboxypeptidase]]	+	*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Carboxypeptidase B~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Pig~~]]	+	[[Category: Sus scrofa]]
-	[[Category: Akparov~~, V K~~]]	+	[[Category: Akparov VK]]
-	[[Category: Kuranova~~, I P~~]]	+	[[Category: Kuranova IP]]
-	[[Category: Timofeev~~, V I]]~~	+	[[Category: Timofeev VI]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:23, 24 October 2018

2018-10-24T06:23:44Z

←Older revision		Revision as of 06:23, 24 October 2018
Line 3:		Line 3:
	<StructureSection load='5jc6' size='340' side='right' caption='[[5jc6]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5jc6' size='340' side='right' caption='[[5jc6]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jc6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JC6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jc6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JC6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPB1, CPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carboxypeptidase_B Carboxypeptidase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.2 3.4.17.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carboxypeptidase_B Carboxypeptidase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.2 3.4.17.2] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc6 OCA], [http://pdbe.org/5jc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jc6 RCSB], [http://www.ebi.ac.uk/pdbsum/5jc6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jc6 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc6 OCA], [http://pdbe.org/5jc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jc6 RCSB], [http://www.ebi.ac.uk/pdbsum/5jc6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jc6 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carboxypeptidase B (EC 3.4.17.2) (CPB) is commonly used in the industrial insulin production and as a template for drug design. However, its ability to discriminate substrates with hydrophobic, hydrophilic, and charged side chains is not well understood. We report structure of CPB complex with a transition state analog N-sulfamoyl-L-phenylalanine solved at 1.74A. The study provided an insight into structural basis of CPB substrate specificity. Ligand binding is affected by structure-depended conformational changes of Asp255 in S1'-subsite, interactions with Asn144 and Arg145 in C-terminal binding subsite, and Glu270 in the catalytic center. Side chain of the non-specific substrate analog SPhe in comparison with that of specific substrate analog SArg (reported earlier) not only loses favorable electrostatic interactions and two hydrogen bonds with Asp255 and three fixed water molecules, but is forced to be in the unfavorable hydrophilic environment. Thus, Ser207, Gly253, Tyr248, and Asp255 residues play major role in the substrate recognition by S1'-subsite.
		+
		+	Structure of the carboxypeptidase B complex with N-sulfamoyl-L-phenylalanine - a transition state analog of non-specific substrate.,Akparov V, Timofeev V, Khaliullin I, Svedas V, Kuranova I J Biomol Struct Dyn. 2018 Mar;36(4):956-965. doi: 10.1080/07391102.2017.1304242. , Epub 2017 Apr 11. PMID:28274181<ref>PMID:28274181</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jc6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carboxypeptidase\|Carboxypeptidase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Carboxypeptidase B]]		[[Category: Carboxypeptidase B]]
		+	[[Category: Pig]]
	[[Category: Akparov, V K]]		[[Category: Akparov, V K]]
	[[Category: Kuranova, I P]]		[[Category: Kuranova, I P]]
	[[Category: Timofeev, V I]]		[[Category: Timofeev, V I]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 13:43, 24 May 2017

2017-05-24T13:43:09Z

←Older revision		Revision as of 13:43, 24 May 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5jc6 ~~is ON HOLD until Apr 14 2018~~	+	==Carboxypeptidase B with 2-nd zinc and acetate ion==
-		+	<StructureSection load='5jc6' size='340' side='right' caption='[[5jc6]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors~~: ~~Timofeev, V~~.I.~~, Akparov, V~~.K.~~, Kuranova, I~~.P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jc6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JC6 FirstGlance]. <br>
-	~~Description~~: Carboxypeptidase B with 2-~~nd zinc and acetate ion~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carboxypeptidase_B Carboxypeptidase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.2 3.4.17.2] </span></td></tr>
-	[[Category: ~~Timofeev~~, V.I]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc6 OCA], [http://pdbe.org/5jc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jc6 RCSB], [http://www.ebi.ac.uk/pdbsum/5jc6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jc6 ProSAT]</span></td></tr>
-	[[Category: Kuranova, I.P]]	+	</table>
-	[[Category: ~~Akparov~~, V.K]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Carboxypeptidase B]]
		+	[[Category: Akparov, V K]]
		+	[[Category: Kuranova, I P]]
		+	[[Category: Timofeev, V I]]
		+	[[Category: Hydrolase]]

OCA at 09:50, 9 March 2017

2017-03-09T09:50:59Z

←Older revision		Revision as of 09:50, 9 March 2017
Line 7:		Line 7:
	Description: Carboxypeptidase B with 2-nd zinc and acetate ion		Description: Carboxypeptidase B with 2-nd zinc and acetate ion
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Timofeev, V.I]]
	[[Category: Kuranova, I.P]]		[[Category: Kuranova, I.P]]
	[[Category: Akparov, V.K]]		[[Category: Akparov, V.K]]
-	[[Category: Timofeev, V.I]]

OCA: Protected "5jc6" [edit=sysop:move=sysop]

2016-05-11T01:50:18Z

Protected "5jc6" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:50, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jc6 is ON HOLD until Apr 14 2018 Authors: Timofeev, V.I., Akparov, V.K., Kuranova, I.P. Description: Carboxypeptidase B with 2-nd zinc and acetate...

2016-05-11T01:50:17Z

New page: '''Unreleased structure''' The entry 5jc6 is ON HOLD until Apr 14 2018 Authors: Timofeev, V.I., Akparov, V.K., Kuranova, I.P. Description: Carboxypeptidase B with 2-nd zinc and acetate...

New page

'''Unreleased structure'''

The entry 5jc6 is ON HOLD until Apr 14 2018

Authors: Timofeev, V.I., Akparov, V.K., Kuranova, I.P.

Description: Carboxypeptidase B with 2-nd zinc and acetate ion
[[Category: Unreleased Structures]]
[[Category: Kuranova, I.P]]
[[Category: Akparov, V.K]]
[[Category: Timofeev, V.I]]