6wvb - Revision history

OCA at 13:16, 6 November 2024

2024-11-06T13:16:39Z

← Older revision		Revision as of 13:16, 6 November 2024
Line 3:		Line 3:
	<StructureSection load='6wvb' size='340' side='right'caption='[[6wvb]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='6wvb' size='340' side='right'caption='[[6wvb]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6wvb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria], [https://en.wikipedia.org/wiki/Escherichia_virus_RB43 Escherichia virus RB43] and [https://en.wikipedia.org/wiki/Takifugu_rubripes Takifugu rubripes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WVB FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WVB FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.872Å</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]] 2.872Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene>, <scene name='pdbligand=SWF:S-WARFARIN'>SWF</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene>, <scene name='pdbligand=SWF:S-WARFARIN'>SWF</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=6wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wvb OCA], [https://pdbe.org/6wvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wvb RCSB], [https://www.ebi.ac.uk/pdbsum/6wvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wvb 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=6wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wvb OCA], [https://pdbe.org/6wvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wvb RCSB], [https://www.ebi.ac.uk/pdbsum/6wvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wvb ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[https://www.uniprot.org/uniprot/VKORL_TAKRU VKORL_TAKRU] Involved in vitamin K metabolism (PubMed:33154105). Can reduce inactive vitamin K 2,3-epoxide to active vitamin K, and may contribute to vitamin K-mediated protection against oxidative stress (PubMed:33154105). Plays a role in vitamin K-dependent gamma-carboxylation of Glu residues in target proteins (By similarity).[UniProtKB:Q8N0U8]<ref>PMID:33154105</ref> [https://www.uniprot.org/uniprot/K0NYR4_9CAUD K0NYR4_9CAUD] [https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Vitamin K antagonists are widely used anticoagulants targeting vitamin K epoxide reductases (VKOR), a family of integral membrane enzymes. To elucidate their catalytic cycle and inhibitory mechanism, here we report eleven x-ray crystal structures of human VKOR and pufferfish VKOR-like with substrates and antagonists in different redox states. Substrates entering the active site in a partially oxidized state form a cysteine adduct that induces an open-to-closed conformational change, triggering reduction. Binding and catalysis is facilitated by hydrogen-bonding interactions in a hydrophobic pocket. The antagonists bind specifically to the same hydrogen-bonding residues and induce a similar closed conformation. Thus, vitamin K antagonists act through mimicking the key interactions and conformational changes required for the VKOR catalytic cycle.

	Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation.,Liu S, Li S, Shen G, Sukumar N, Krezel AM, Li W Science. 2020 Nov 5. pii: science.abc5667. doi: 10.1126/science.abc5667. PMID:33154105<ref>PMID:33154105</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6wvb" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]		*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Aequorea victoria]]~~
	~~[[Category: Escherichia virus RB43]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Takifugu rubripes]]~~
	[[Category: Li W]]		[[Category: Li W]]
	[[Category: Liu S]]		[[Category: Liu S]]
	[[Category: Sukumar N]]		[[Category: Sukumar N]]

OCA at 14:37, 18 October 2023

2023-10-18T14:37:46Z

← Older revision		Revision as of 14:37, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='6wvb' size='340' side='right'caption='[[6wvb]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='6wvb' size='340' side='right'caption='[[6wvb]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6wvb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aeqvi Aeqvi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6wvb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria], [https://en.wikipedia.org/wiki/Escherichia_virus_RB43 Escherichia virus RB43] and [https://en.wikipedia.org/wiki/Takifugu_rubripes Takifugu rubripes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WVB FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SWF:S~~-~~WARFARIN'>SWF</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]] 2.872Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene>, <scene name='pdbligand=SWF:S-WARFARIN'>SWF</scene></td></tr>
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">gfp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])~~</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=6wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wvb OCA], [https://pdbe.org/6wvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wvb RCSB], [https://www.ebi.ac.uk/pdbsum/6wvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wvb 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=6wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wvb OCA], [~~http~~://pdbe.org/6wvb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wvb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wvb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wvb ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/VKORL_TAKRU VKORL_TAKRU] Involved in vitamin K metabolism (PubMed:33154105). Can reduce inactive vitamin K 2,3-epoxide to active vitamin K, and may contribute to vitamin K-mediated protection against oxidative stress (PubMed:33154105). Plays a role in vitamin K-dependent gamma-carboxylation of Glu residues in target proteins (By similarity).[UniProtKB:Q8N0U8]<ref>PMID:33154105</ref> [https://www.uniprot.org/uniprot/K0NYR4_9CAUD K0NYR4_9CAUD] [https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6wvb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6wvb" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Aeqvi~~]]		[[Category: Aequorea victoria]]
			[[Category: Escherichia virus RB43]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Li, W~~]]		[[Category: Takifugu rubripes]]
	[[Category: ~~Liu, S~~]]		[[Category: Li W]]
	[[Category: ~~Sukumar, N~~]]		[[Category: Liu S]]
	[[Category: ~~Membrane protein]]~~		[[Category: Sukumar N]]
	~~[[Category: Vitamin k epoxide reductase]]~~
	~~[[Category: Vkor]]~~
	~~[[Category: Vkor-like protein]]~~
	~~[[Category: Vkorl~~]]

OCA at 07:11, 25 November 2020

2020-11-25T07:11:17Z

← Older revision		Revision as of 07:11, 25 November 2020
Line 1:		Line 1:

	==Takifugu rubripes VKOR-like with warfarin==		==Takifugu rubripes VKOR-like with warfarin==
	<StructureSection load='6wvb' size='340' side='right'caption='[[6wvb]]' scene=''>		<StructureSection load='6wvb' size='340' side='right'caption='[[6wvb]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WVB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6wvb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WVB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WVB FirstGlance]. <br>
	</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=6wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wvb OCA], [http://pdbe.org/6wvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wvb RCSB], [http://www.ebi.ac.uk/pdbsum/6wvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wvb ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SWF:S-WARFARIN'>SWF</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gfp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])</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=6wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wvb OCA], [http://pdbe.org/6wvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wvb RCSB], [http://www.ebi.ac.uk/pdbsum/6wvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wvb ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Vitamin K antagonists are widely used anticoagulants targeting vitamin K epoxide reductases (VKOR), a family of integral membrane enzymes. To elucidate their catalytic cycle and inhibitory mechanism, here we report eleven x-ray crystal structures of human VKOR and pufferfish VKOR-like with substrates and antagonists in different redox states. Substrates entering the active site in a partially oxidized state form a cysteine adduct that induces an open-to-closed conformational change, triggering reduction. Binding and catalysis is facilitated by hydrogen-bonding interactions in a hydrophobic pocket. The antagonists bind specifically to the same hydrogen-bonding residues and induce a similar closed conformation. Thus, vitamin K antagonists act through mimicking the key interactions and conformational changes required for the VKOR catalytic cycle.

			Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation.,Liu S, Li S, Shen G, Sukumar N, Krezel AM, Li W Science. 2020 Nov 5. pii: science.abc5667. doi: 10.1126/science.abc5667. PMID:33154105<ref>PMID:33154105</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6wvb" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Aeqvi]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Li W]]		[[Category: Li, W]]
	[[Category: Liu S]]		[[Category: Liu, S]]
	[[Category: Sukumar N]]		[[Category: Sukumar, N]]
			[[Category: Membrane protein]]
			[[Category: Vitamin k epoxide reductase]]
			[[Category: Vkor]]
			[[Category: Vkor-like protein]]
			[[Category: Vkorl]]

OCA at 08:00, 11 November 2020

2020-11-11T08:00:01Z

← Older revision		Revision as of 08:00, 11 November 2020
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6wvb is ~~ON HOLD until May 05 2022~~		==Takifugu rubripes VKOR-like with warfarin==
			<StructureSection load='6wvb' size='340' side='right'caption='[[6wvb]]' scene=''>
	~~Authors~~: ~~Liu~~, S., ~~Sukumar~~, N., Li, W.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WVB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WVB FirstGlance]. <br>
	~~Description: Takifugu rubripes VKOR-like with warfarin~~		</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=6wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wvb OCA], [http://pdbe.org/6wvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wvb RCSB], [http://www.ebi.ac.uk/pdbsum/6wvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wvb ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Sukumar, N~~]]		__TOC__
	[[Category: Liu, S]]		</StructureSection>
	[[Category: ~~Li, W~~]]		[[Category: Large Structures]]
			[[Category: Li W]]
			[[Category: Liu S]]
			[[Category: Sukumar N]]

OCA at 04:52, 10 June 2020

2020-06-10T04:52:50Z

← Older revision		Revision as of 04:52, 10 June 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6wvb is ON HOLD		The entry 6wvb is ON HOLD until May 05 2022

	Authors: Liu, S., Sukumar, N., Li, W.		Authors: Liu, S., Sukumar, N., Li, W.

OCA: Protected "6wvb" [edit=sysop:move=sysop]

2020-05-13T04:11:02Z

Protected "6wvb" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:11, 13 May 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6wvb is ON HOLD Authors: Liu, S., Sukumar, N., Li, W. Description: Takifugu rubripes VKOR-like with warfarin Category: Unreleased Structures [[...

2020-05-13T04:11:01Z

New page: '''Unreleased structure''' The entry 6wvb is ON HOLD Authors: Liu, S., Sukumar, N., Li, W. Description: Takifugu rubripes VKOR-like with warfarin Category: Unreleased Structures [[...

New page

'''Unreleased structure'''

The entry 6wvb is ON HOLD

Authors: Liu, S., Sukumar, N., Li, W.

Description: Takifugu rubripes VKOR-like with warfarin
[[Category: Unreleased Structures]]
[[Category: Sukumar, N]]
[[Category: Liu, S]]
[[Category: Li, W]]