1vit

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:17, 3 April 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1vit.gif|left|200px]]
 
-
<!--
+
==THROMBIN:HIRUDIN 51-65 COMPLEX==
-
The line below this paragraph, containing "STRUCTURE_1vit", creates the "Structure Box" on the page.
+
<StructureSection load='1vit' size='340' side='right'caption='[[1vit]], [[Resolution|resolution]] 3.20&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'>[[1vit]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VIT 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]] 3.2&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-
{{STRUCTURE_1vit| PDB=1vit | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vit OCA], [https://pdbe.org/1vit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vit RCSB], [https://www.ebi.ac.uk/pdbsum/1vit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vit ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/THRB_BOVIN THRB_BOVIN] 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 (By similarity).
 +
== 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/vi/1vit_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=1vit ConSurf].
 +
<div style="clear:both"></div>
-
'''THROMBIN:HIRUDIN 51-65 COMPLEX'''
+
==See Also==
-
 
+
*[[Hirudin 3D structures|Hirudin 3D structures]]
-
 
+
*[[Thrombin 3D Structures|Thrombin 3D Structures]]
-
==Overview==
+
__TOC__
-
Crystals of the bovine thrombin-hirudins(51-65) complex have space group P6(1)22 with cell constants a = 116.4, and c = 200.6 A and two thrombin molecules in the asymmetric unit. Only one thrombin molecule could be located by generalized molecular replacement; the second was fit visually as a rigid body to an improved electron-density difference map. The structure was refined to R = 0.192 with two B values per residue (main chain and side chain) at 3.2 A. The polar interactions of the peptides with the exosite of thrombin show differences consistent with the known flexibility in the interactions of the C-terminal peptide of hirudin with thrombin. The hirudin peptide in complex 2 has a higher temperature factor as compared with peptide 1 which may be correlated partly with a larger number of short-range electrostatic interactions between peptide 1 and thrombin and partly with the fact that thrombin 2 is epsilon-thrombin which is cleaved at Thr149A near the peptide binding site. Later, using this structure as a test case, it was shown that the position for the second thrombin could also be determined by a novel modification of the molecular-replacement method in which the contribution of the known molecule is subtracted from the structure factors. This approach is facile and applicable to any crystal containing two or more macromolecules in the asymmetric unit in which some but not all of the molecules can be determined by molecular replacement.
+
</StructureSection>
-
 
+
-
==About this Structure==
+
-
1VIT is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIT OCA].
+
-
 
+
-
==Reference==
+
-
Structure of a bovine thrombin-hirudin51-65 complex determined by a combination of molecular replacement and graphics. Incorporation of known structural information in molecular replacement., Vitali J, Martin PD, Malkowski MG, Olsen CM, Johnson PH, Edwards BF, Acta Crystallogr D Biol Crystallogr. 1996 May 1;52(Pt 3):453-64. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15299666 15299666]
+
[[Category: Bos taurus]]
[[Category: Bos taurus]]
-
[[Category: Protein complex]]
+
[[Category: Large Structures]]
-
[[Category: Thrombin]]
+
[[Category: Edwards BFP]]
-
[[Category: Edwards, B F.P.]]
+
[[Category: Vitali J]]
-
[[Category: Vitali, J.]]
+
-
[[Category: Blood coagulation]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Serine protease]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 12:34:44 2008''
+

Current revision

THROMBIN:HIRUDIN 51-65 COMPLEX

PDB ID 1vit

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/1vit"
Personal tools