8f6m - Revision history

OCA at 10:31, 25 October 2023

OCA — Wed, 25 Oct 2023 10:31:54 GMT

←Older revision		Revision as of 10:31, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8f6m]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8F6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8F6M FirstGlance]. <br>		<table><tr><td colspan='2'>[[8f6m]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8F6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8F6M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GZ3:(E)-2-METHYL-3-PHOSPHONOACRYLATE'>GZ3</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 2.15Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GZ3:(E)-2-METHYL-3-PHOSPHONOACRYLATE'>GZ3</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></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=8f6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8f6m OCA], [https://pdbe.org/8f6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8f6m RCSB], [https://www.ebi.ac.uk/pdbsum/8f6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8f6m ProSAT]</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=8f6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8f6m OCA], [https://pdbe.org/8f6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8f6m RCSB], [https://www.ebi.ac.uk/pdbsum/8f6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8f6m ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 8f6m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 8f6m" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pyruvate kinase 3D structures\|Pyruvate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:05, 25 May 2023

OCA — Thu, 25 May 2023 04:05:26 GMT

←Older revision		Revision as of 04:05, 25 May 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8f6m is ~~ON HOLD until Paper~~ Publication	+	==Complex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP mimicking the Michaelis complex.==
		+	<StructureSection load='8f6m' size='340' side='right'caption='[[8f6m]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8f6m]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8F6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8F6M FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GZ3:(E)-2-METHYL-3-PHOSPHONOACRYLATE'>GZ3</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></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=8f6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8f6m OCA], [https://pdbe.org/8f6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8f6m RCSB], [https://www.ebi.ac.uk/pdbsum/8f6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8f6m ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KPYM_RABIT KPYM_RABIT] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family-pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization-including quantitative evaluation of allosteric regulation-of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms. Database URL https://github.com/djparente/PYK-DB.

-	~~Authors~~:	+	PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes.,Swint-Kruse L, Dougherty LL, Page B, Wu T, O'Neil PT, Prasannan CB, Timmons C, Tang Q, Parente DJ, Sreenivasan S, Holyoak T, Fenton AW Database (Oxford). 2023 May 3;2023:baad030. doi: 10.1093/database/baad030. PMID:37171062<ref>PMID:37171062</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8f6m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Oryctolagus cuniculus]]
		+	[[Category: Fenton AW]]
		+	[[Category: Holyoak T]]

OCA at 06:30, 21 December 2022

OCA — Wed, 21 Dec 2022 06:30:58 GMT

←Older revision		Revision as of 06:30, 21 December 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8f6m is ON HOLD	+	The entry 8f6m is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8f6m" [edit=sysop:move=sysop]

OCA — Thu, 24 Nov 2022 08:17:06 GMT

Protected "8f6m" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:17, 24 November 2022

OCA: New page: '''Unreleased structure''' The entry 8f6m is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 24 Nov 2022 08:17:03 GMT

New page: '''Unreleased structure''' The entry 8f6m is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8f6m is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]