1ucy: Difference between revisions

Revision as of 16:23, 21 February 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a fibrinogen-A alpha tridecapeptide substrate analog, G17 psi, in which the scissile bond amide nitrogen of Gly-17f has been replaced by a methylene carbon, has been determined at 2.3 A resolution with an R factor of 17.1%.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 with as ligand. Active as Thrombin, with EC number 3.4.21.5 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 Thu Feb 21 15:23:11 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1ucy.jpg|left|200px]]<br /><applet load="1ucy" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1ucy.jpg|left|200px]]<br /><applet load="1ucy" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1ucy, resolution 2.2&Aring;" />
 '''THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN'''<br />
 ==Overview==
-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.
+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 Structure==
-UCY is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with ACE as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UCY OCA].
+UCY is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with <scene name='pdbligand=ACE:'>ACE</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UCY OCA].
 ==Reference==
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 [[Category: thrombin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:01:51 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:23:11 2008''