1iod: Difference between revisions

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-[[Image:1iod.gif|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X==
-|PDB= 1iod |SIZE=350|CAPTION= <scene name='initialview01'>1iod</scene>, resolution 2.3&Aring;
+<StructureSection load='1iod' size='340' side='right'caption='[[1iod]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>
+<table><tr><td colspan='2'>[[1iod]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Deinagkistrodon_acutus Deinagkistrodon acutus]. The March 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Tissue Factor''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_3 10.2210/rcsb_pdb/mom_2006_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IOD FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_Xa Coagulation factor Xa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.6 3.4.21.6] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1iod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iod OCA], [https://pdbe.org/1iod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iod RCSB], [https://www.ebi.ac.uk/pdbsum/1iod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iod ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1ixx|1IXX]], [[1bj3|1BJ3]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iod OCA], [http://www.ebi.ac.uk/pdbsum/1iod PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1iod RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/SLUA_DEIAC SLUA_DEIAC] Anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factors IX (F9) and factor X (F10) in the presence of calcium with a 1 to 1 stoichiometry. Also inhibits platelet aggregation by binding to platelet glycoprotein Ibalpha (GP1BA) and functioning as a blocker of von Willebrand factor (VWF). Is devoid of hemorrhagic and lethal activities. Possesses antithrombotic and thrombolytic activities. Also hydrolyzes the Aalpha-chain of fibrinogen (FGA). Does not affect the Bbeta-chain (FGB) and the gamma chain (FGG).<ref>PMID:10558903</ref> <ref>PMID:12058182</ref> <ref>PMID:15925567</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/io/1iod_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1iod ConSurf].
+<div style="clear:both"></div>
-'''CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X'''
+==See Also==
+*[[Factor Xa|Factor Xa]]
+== References ==
-==Overview==
+<references/>
-The gamma-carboxyglutamic acid (Gla) domain of blood coagulation factors is responsible for Ca2+-dependent phospholipid membrane binding. Factor X-binding protein (X-bp), an anticoagulant protein from snake venom, specifically binds to the Gla domain of factor X. The crystal structure of X-bp in complex with the Gla domain peptide of factor X at 2.3-A resolution showed that the anticoagulation is based on the fact that two patches of the Gla domain essential for membrane binding are buried in the complex formation. The Gla domain thus is expected to be a new target of anticoagulant drugs, and X-bp provides a basis for designing them. This structure also provides a membrane-bound model of factor X.
+__TOC__
+</StructureSection>
-==About this Structure==
-IOD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Deinagkistrodon_acutus Deinagkistrodon acutus]. The following page contains interesting information on the relation of 1IOD with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb75_1.html Tissue Factor]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IOD OCA].
-==Reference==
-Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X., Mizuno H, Fujimoto Z, Atoda H, Morita T, Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7230-4. Epub 2001 Jun 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11404471 11404471]
 [[Category: Bos taurus]]
-[[Category: Coagulation factor Xa]]
 [[Category: Deinagkistrodon acutus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
+[[Category: RCSB PDB Molecule of the Month]]
 [[Category: Tissue Factor]]
-[[Category: Atoda, H.]]
+[[Category: Atoda H]]
-[[Category: Fujimoto, Z.]]
+[[Category: Fujimoto Z]]
-[[Category: Mizuno, H.]]
+[[Category: Mizuno H]]
-[[Category: Morita, T.]]
+[[Category: Morita T]]
-[[Category: calcium bridging]]
-[[Category: domain swapping]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:22:31 2008''