1iod: Difference between revisions

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New page: left|200px<br /> <applet load="1iod" size="450" color="white" frame="true" align="right" spinBox="true" caption="1iod, resolution 2.3Å" /> '''CRYSTAL STRUCTURE OF...
 
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[[Image:1iod.gif|left|200px]]<br />
<applet load="1iod" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1iod, resolution 2.3&Aring;" />
'''CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X'''<br />


==Overview==
==CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X==
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.
<StructureSection load='1iod' size='340' side='right'caption='[[1iod]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== 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>


==About this Structure==
==See Also==
1IOD is a [http://en.wikipedia.org/wiki/Single_protein 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] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. 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]]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IOD OCA].
*[[Factor Xa|Factor Xa]]
 
== References ==
==Reference==
<references/>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=11404471 11404471]
__TOC__
</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Coagulation factor Xa]]
[[Category: Deinagkistrodon acutus]]
[[Category: Deinagkistrodon acutus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Tissue Factor]]
[[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: CA]]
[[Category: calcium bridging]]
[[Category: domain swapping]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:01:56 2007''

Latest revision as of 09:02, 3 April 2024

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR XCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X

Structural highlights

1iod is a 3 chain structure with sequence from Bos taurus and Deinagkistrodon acutus. The March 2006 RCSB PDB Molecule of the Month feature on Tissue Factor by David S. Goodsell is 10.2210/rcsb_pdb/mom_2006_3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).[1] [2] [3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Cheng X, Qian Y, Liu Q, Li BX, Zhang M, Liu J. Purification, characterization, and cDNA cloning of a new fibrinogenlytic venom protein, Agkisacutacin, from Agkistrodon acutus venom. Biochem Biophys Res Commun. 1999 Nov 19;265(2):530-5. PMID:10558903 doi:10.1006/bbrc.1999.1685
  2. ↑ Cheng X, Xu ZY, Liu QD, Li XM, Li XY, Liu J. Purification and Characterization of a Platelet Agglutinating Inhibiting Protein (Agkisacutacin) from Agkistrodon acutus Venom. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 2000;32(6):653-656 PMID:12058182
  3. ↑ Li WF, Chen L, Li XM, Liu J. A C-type lectin-like protein from Agkistrodon acutus venom binds to both platelet glycoprotein Ib and coagulation factor IX/factor X. Biochem Biophys Res Commun. 2005 Jul 8;332(3):904-12. PMID:15925567 doi:10.1016/j.bbrc.2005.05.033

1iod, resolution 2.30Å

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