5gv8 - Revision history

OCA at 11:43, 2 August 2023

OCA — Wed, 02 Aug 2023 11:43:36 GMT

←Older revision		Revision as of 11:43, 2 August 2023
Line 3:		Line 3:
	<StructureSection load='5gv8' size='340' side='right'caption='[[5gv8]], [[Resolution\|resolution]] 0.78Å' scene=''>		<StructureSection load='5gv8' size='340' side='right'caption='[[5gv8]], [[Resolution\|resolution]] 0.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gv8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GV8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GV8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gv8]] 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=5GV8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GV8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 0.78Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5gv7\|5gv7]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2]~~ </~~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=5gv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gv8 OCA], [https://pdbe.org/5gv8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gv8 RCSB], [https://www.ebi.ac.uk/pdbsum/5gv8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gv8 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5gv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gv8 OCA], [~~http~~://pdbe.org/5gv8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gv8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gv8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gv8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG]] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]	+	[https://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cytochrome-b5 reductase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Miki, K~~]]	+	[[Category: Sus scrofa]]
-	[[Category: ~~Takaba,~~ K]]	+	[[Category: Miki K]]
-	[[Category: ~~Takeda,~~ K]]	+	[[Category: Takaba K]]
-	[[Category: ~~Electron transfer]]~~	+	[[Category: Takeda K]]
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:44, 20 May 2020

OCA — Wed, 20 May 2020 06:44:10 GMT

←Older revision		Revision as of 06:44, 20 May 2020
Line 1:		Line 1:

	==Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.78A==		==Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.78A==
-	<StructureSection load='5gv8' size='340' side='right' caption='[[5gv8]], [[Resolution\|resolution]] 0.78Å' scene=''>	+	<StructureSection load='5gv8' size='340' side='right'caption='[[5gv8]], [[Resolution\|resolution]] 0.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gv8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GV8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GV8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gv8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GV8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GV8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gv7\|5gv7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gv7\|5gv7]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2] </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=5gv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gv8 OCA], [http://pdbe.org/5gv8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gv8 RCSB], [http://www.ebi.ac.uk/pdbsum/5gv8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gv8 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gv8 OCA], [http://pdbe.org/5gv8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gv8 RCSB], [http://www.ebi.ac.uk/pdbsum/5gv8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gv8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5gv8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gv8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[NADH-cytochrome b5 reductase\|NADH-cytochrome b5 reductase]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Cytochrome-b5 reductase]]		[[Category: Cytochrome-b5 reductase]]
		+	[[Category: Large Structures]]
	[[Category: Miki, K]]		[[Category: Miki, K]]
	[[Category: Takaba, K]]		[[Category: Takaba, K]]

OCA at 13:18, 5 April 2017

OCA — Wed, 05 Apr 2017 13:18:33 GMT

←Older revision		Revision as of 13:18, 5 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gv8 is ~~ON HOLD~~	+	==Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.78A==
		+	<StructureSection load='5gv8' size='340' side='right' caption='[[5gv8]], [[Resolution\|resolution]] 0.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gv8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GV8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GV8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gv7\|5gv7]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2] </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=5gv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gv8 OCA], [http://pdbe.org/5gv8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gv8 RCSB], [http://www.ebi.ac.uk/pdbsum/5gv8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gv8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG]] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Flavin compounds such as flavin adenine dinucleotide (FAD), flavin mononucleotide and riboflavin make up the active centers in flavoproteins that facilitate various oxidoreductive processes. The fine structural features of the hydrogens and valence electrons of the flavin molecules in the protein environment are critical to the functions of the flavoproteins. However, information on these features cannot be obtained from conventional protein X-ray analyses at ordinary resolution. Here we report the charge density analysis of a flavoenzyme, NADH-cytochrome b5 reductase (b5R), at an ultra-high resolution of 0.78 A. Valence electrons on the FAD cofactor as well as the peptide portion, which are clearly visualized even after the conventional refinement, are analyzed by the multipolar atomic model refinement. The topological analysis for the determined electron density reveals the valence electronic structure of the isoalloxazine ring of FAD and hydrogen-bonding interactions with the protein environment. The tetrahedral electronic distribution around the N5 atom of FAD in b5R is stabilized by hydrogen bonding with CalphaH of Tyr65 and amide-H of Thr66. The hydrogen bonding network leads to His49 composing the cytochrome b5-binding site via non-classical hydrogen bonds between N5 of FAD and CalphaH of Tyr65 and O of Tyr65 and CbetaH of His49.

-	~~Authors: Takaba~~, K., Takeda, K., ~~Miki~~, K.	+	Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase.,Takaba K, Takeda K, Kosugi M, Tamada T, Miki K Sci Rep. 2017 Feb 22;7:43162. doi: 10.1038/srep43162. PMID:28225078<ref>PMID:28225078</ref>

-	~~Description: Structure~~ of ~~NADH-cytochrome b5 reductase refined with~~ the ~~multipolar atomic model at 0~~.~~78A~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Takeda, K~~]]	+	<div class="pdbe-citations 5gv8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cytochrome-b5 reductase]]
	[[Category: Miki, K]]		[[Category: Miki, K]]
	[[Category: Takaba, K]]		[[Category: Takaba, K]]
		+	[[Category: Takeda, K]]
		+	[[Category: Electron transfer]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5gv8" [edit=sysop:move=sysop]

OCA — Wed, 14 Sep 2016 10:31:12 GMT

Protected "5gv8" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:31, 14 September 2016

OCA: New page: '''Unreleased structure''' The entry 5gv8 is ON HOLD Authors: Takaba, K., Takeda, K., Miki, K. Description: Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic...

OCA — Wed, 14 Sep 2016 10:31:11 GMT

New page: '''Unreleased structure''' The entry 5gv8 is ON HOLD Authors: Takaba, K., Takeda, K., Miki, K. Description: Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic...

New page

'''Unreleased structure'''

The entry 5gv8 is ON HOLD

Authors: Takaba, K., Takeda, K., Miki, K.

Description: Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.78A
[[Category: Unreleased Structures]]
[[Category: Takeda, K]]
[[Category: Miki, K]]
[[Category: Takaba, K]]