6wvb: Difference between revisions

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<StructureSection load='6wvb' size='340' side='right'caption='[[6wvb]], [[Resolution|resolution]] 2.87&Aring;' scene=''>
<StructureSection load='6wvb' size='340' side='right'caption='[[6wvb]], [[Resolution|resolution]] 2.87&Aring;' 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]] 2.872&#8491;</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]] 2.872&#8491;</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&reg;/PubMed&reg;, 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]]

Latest revision as of 16:16, 6 November 2024

Takifugu rubripes VKOR-like with warfarinTakifugu rubripes VKOR-like with warfarin

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.872Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

6wvb, resolution 2.87Å

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