3da9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:36, 3 April 2024) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3da9.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of thrombin in complex with inhibitor==
-
The line below this paragraph, containing "STRUCTURE_3da9", creates the "Structure Box" on the page.
+
<StructureSection load='3da9' size='340' side='right'caption='[[3da9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3da9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DA9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DA9 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=44U:BETA-PHENYL-D-PHENYLALANYL-N-PROPYL-L-PROLINAMIDE'>44U</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
-
{{STRUCTURE_3da9| PDB=3da9 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3da9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3da9 OCA], [https://pdbe.org/3da9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3da9 RCSB], [https://www.ebi.ac.uk/pdbsum/3da9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3da9 ProSAT]</span></td></tr>
 +
</table>
 +
== Disease ==
 +
[https://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[https://omim.org/entry/613679 613679]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[https://omim.org/entry/601367 601367]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[https://omim.org/entry/188050 188050]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[https://omim.org/entry/614390 614390]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.<ref>PMID:2856554</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/da/3da9_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=3da9 ConSurf].
 +
<div style="clear:both"></div>
-
===Crystal structure of thrombin in complex with inhibitor===
+
==See Also==
-
 
+
*[[Hirudin 3D structures|Hirudin 3D structures]]
-
 
+
*[[Thrombin 3D Structures|Thrombin 3D Structures]]
-
<!--
+
== References ==
-
The line below this paragraph, {{ABSTRACT_PUBMED_19371038}}, adds the Publication Abstract to the page
+
<references/>
-
(as it appears on PubMed at http://www.pubmed.gov), where 19371038 is the PubMed ID number.
+
__TOC__
-
-->
+
</StructureSection>
-
{{ABSTRACT_PUBMED_19371038}}
+
-
 
+
-
==About this Structure==
+
-
3DA9 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DA9 OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:19371038</ref><references group="xtra"/>
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Thrombin]]
+
[[Category: Large Structures]]
-
[[Category: Hansson, S K.]]
+
[[Category: Hansson SK]]
-
[[Category: Xue, Y.]]
+
[[Category: Xue Y]]
-
[[Category: Acute phase]]
+
-
[[Category: Blood coagulation]]
+
-
[[Category: Calcium]]
+
-
[[Category: Cleavage on pair of basic residue]]
+
-
[[Category: Disease mutation]]
+
-
[[Category: Gamma-carboxyglutamic acid]]
+
-
[[Category: Glycoprotein]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Inhibitor complex]]
+
-
[[Category: Kringle]]
+
-
[[Category: Pharmaceutical]]
+
-
[[Category: Polymorphism]]
+
-
[[Category: Protease]]
+
-
[[Category: Secreted]]
+
-
[[Category: Serine protease]]
+
-
[[Category: Thrombin]]
+
-
[[Category: Zymogen]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 17:01:12 2009''
+

Current revision

Crystal structure of thrombin in complex with inhibitor

PDB ID 3da9

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3da9"
Personal tools