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.


Sandbox Reserved 348

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(Added a real image, scene tweaks)
m (Tweak 3D structures section)
Line 13: Line 13:
Thrombin is comprised of two chains, often referred to as the <scene name='Sandbox_Reserved_348/Small_subunit/2'>short chain</scene> and the <scene name='Sandbox_Reserved_348/Large_subunit/2'>long chain</scene>. There is one <scene name='Sandbox_Reserved_348/Ligand/2'>active site</scene>, which in the case of [[1ppb]] is occupied with D-Phe-Pro-Arg chloromethylketone.<ref name="The refined 1.9A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.">PMID:2583108</ref> Additionally, there are three structural disulfide bonds.
Thrombin is comprised of two chains, often referred to as the <scene name='Sandbox_Reserved_348/Small_subunit/2'>short chain</scene> and the <scene name='Sandbox_Reserved_348/Large_subunit/2'>long chain</scene>. There is one <scene name='Sandbox_Reserved_348/Ligand/2'>active site</scene>, which in the case of [[1ppb]] is occupied with D-Phe-Pro-Arg chloromethylketone.<ref name="The refined 1.9A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.">PMID:2583108</ref> Additionally, there are three structural disulfide bonds.
-
==3D Structures of α-Thrombin==
+
==3D Structures==
 +
===α-Thrombin===
*[[1ppb]]
*[[1ppb]]
*[[1uma]]
*[[1uma]]
*[[1de7]]
*[[1de7]]
-
==3D Structures of Prothrombin==
+
===Prothrombin===
*[[2afq]]
*[[2afq]]

Revision as of 05:00, 27 March 2011

This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada.
To get started:
  • Click the edit this page tab at the top. Save the page after each step, then edit it again.
  • Click the 3D button (when editing, above the wikitext box) to insert Jmol.
  • show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
  • Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing


PDB ID 1ppb

Drag the structure with the mouse to rotate
1ppb, resolution 1.92Å ()
Ligands:
Activity: Thrombin, with EC number 3.4.21.5
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


The role of thrombin and prothrombin in coagulation.
The role of thrombin and prothrombin in coagulation.

Thrombin is a trypsin-like serine protease which is best known for its role in blood clotting. In humans, the F2 gene codes for prothrombin, which is also known as Coagulation Factor II.[1][2] Clevage of prothrombin to form activated α-thrombin is a key step in the final common pathway of blood clotting, because thrombin activates fibrin, which creates cross-linked fibrin clots.[3]

Contents


Structure

Thrombin is comprised of two chains, often referred to as the and the . There is one , which in the case of 1ppb is occupied with D-Phe-Pro-Arg chloromethylketone.[4] Additionally, there are three structural disulfide bonds.

3D Structures

α-Thrombin

Prothrombin

See Also

External Resources

References

  1. ↑ Royle NJ, Irwin DM, Koschinsky ML, MacGillivray RT, Hamerton JL. Human genes encoding prothrombin and ceruloplasmin map to 11p11-q12 and 3q21-24, respectively. Somat Cell Mol Genet. 1987 May;13(3):285-92. PMID:3474786
  2. ↑ Degen SJ, Davie EW. Nucleotide sequence of the gene for human prothrombin. Biochemistry. 1987 Sep 22;26(19):6165-77. PMID:2825773
  3. ↑ Di Cera E. Thrombin interactions. Chest. 2003 Sep;124(3 Suppl):11S-7S. PMID:12970119
  4. ↑ Bode W, Mayr I, Baumann U, Huber R, Stone SR, Hofsteenge J. The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment. EMBO J. 1989 Nov;8(11):3467-75. PMID:2583108
Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_348"
Personal tools