This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1nl1

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:30, 7 February 2018

BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION

Structural highlights

1nl1 is a 1 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Related:	2pf2
Activity:	Thrombin, with EC number 3.4.21.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

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

Publication Abstract from PubMed

In a calcium-dependent interaction critical for blood coagulation, vitamin K-dependent blood coagulation proteins bind cell membranes containing phosphatidylserine via gamma-carboxyglutamic acid-rich (Gla) domains. Gla domain-mediated protein-membrane interaction is required for generation of thrombin, the terminal enzyme in the coagulation cascade, on a physiologic time scale. We determined by X-ray crystallography and NMR spectroscopy the lysophosphatidylserine-binding site in the bovine prothrombin Gla domain. The serine head group binds Gla domain-bound calcium ions and Gla residues 17 and 21, fixed elements of the Gla domain fold, predicting the structural basis for phosphatidylserine specificity among Gla domains. Gla domains provide a unique mechanism for protein-phospholipid membrane interaction. Increasingly Gla domains are being identified in proteins unrelated to blood coagulation. Thus, this membrane-binding mechanism may be important in other physiologic processes.

Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins.,Huang M, Rigby AC, Morelli X, Grant MA, Huang G, Furie B, Seaton B, Furie BC Nat Struct Biol. 2003 Sep;10(9):751-6. Epub 2003 Aug 17. PMID:12923575^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Huang M, Rigby AC, Morelli X, Grant MA, Huang G, Furie B, Seaton B, Furie BC. Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins. Nat Struct Biol. 2003 Sep;10(9):751-6. Epub 2003 Aug 17. PMID:12923575 doi:http://dx.doi.org/10.1038/nsb971

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nl1"

@@ Line 1: / Line 1: @@
 ==BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION==
 <StructureSection load='1nl1' size='340' side='right' caption='[[1nl1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2pf2|2pf2]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nl1 OCA], [http://pdbe.org/1nl1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nl1 RCSB], [http://www.ebi.ac.uk/pdbsum/1nl1 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nl1 OCA], [http://pdbe.org/1nl1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nl1 RCSB], [http://www.ebi.ac.uk/pdbsum/1nl1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nl1 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nl/1nl1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nl/1nl1_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 31: @@
 </div>
 <div class="pdbe-citations 1nl1" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Thrombin|Thrombin]]
 == References ==
 <references/>

1nl1

From Proteopedia

Revision as of 07:30, 7 February 2018

BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox