1ucy: Difference between revisions

Revision as of 11:03, 3 May 2008

THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN

OverviewOverview

The crystal structure of the noncovalent complex of bovine thrombin and a fibrinogen-A alpha tridecapeptide substrate analog, G17 psi, in which the scissile bond amide nitrogen of Gly-17f has been replaced by a methylene carbon, has been determined at 2.3 A resolution with an R factor of 17.1%. The geometry of the active site indicates that the crystal structure is a close model of the true Michaelis complex. The three independently determined thrombin/G17 psi complexes in the crystal asymmetric unit reveal novel interactions for the P2' and P3' residues-Pro-18f and Arg-19f, respectively-on the carboxyl-terminal side of the scissile bond and confirm previously observed interactions of the P1 (Arg-16f) through P10 (Asp-7f) positions on the amino-terminal side. The thrombin S2' binding site for Pro-18f, as observed in all three complexes, differs from that predicted by modeling studies and is notable for including two carbonyl oxygens of the thrombin main chain. Arg-19f occupies two binding sites on thrombin, S3'A and S3'B, which have dramatically different placements for the arginyl side chain and carboxyl terminus.

About this StructureAbout this Structure

1UCY is a Protein complex structure of sequences from Bos taurus. Full crystallographic information is available from OCA.

ReferenceReference

Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues., Martin PD, Malkowski MG, DiMaio J, Konishi Y, Ni F, Edwards BF, Biochemistry. 1996 Oct 8;35(40):13030-9. PMID:8855938 Page seeded by OCA on Sat May 3 11:03:19 2008

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OCA

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 [[Image:1ucy.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 1ucy |SIZE=350|CAPTION= <scene name='initialview01'>1ucy</scene>, resolution 2.2&Aring;
+The line below this paragraph, containing "STRUCTURE_1ucy", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=OPR:C-(3-OXOPROPYL)ARGININE'>OPR</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <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>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1ucy|  PDB=1ucy  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ucy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ucy OCA], [http://www.ebi.ac.uk/pdbsum/1ucy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ucy RCSB]</span>
-}}
 '''THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN'''
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 [[Category: Edwards, B.]]
 [[Category: Martin, P.]]
-[[Category: complex (serine protease/coagulation)]]
+[[Category: Protease]]
-[[Category: protease]]
+[[Category: Serine]]
-[[Category: serine]]
+[[Category: Thrombin]]
-[[Category: thrombin]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 11:03:19 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:08:41 2008''