1bk9

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[[Image:1bk9.jpg|left|200px]]<br /><applet load="1bk9" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1bk9.jpg|left|200px]]
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caption="1bk9, resolution 2.00&Aring;" />
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'''PHOSPHOLIPASE A2 MODIFIED BY PBPB'''<br />
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{{Structure
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|PDB= 1bk9 |SIZE=350|CAPTION= <scene name='initialview01'>1bk9</scene>, resolution 2.00&Aring;
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|SITE= <scene name='pdbsite=PBP:P-Bromo-Phenacyl-Bromide+Covalently+Binding+w.+Nd1+Of+HIS+48'>PBP</scene>
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PBP:1-(4-BROMO-PHENYL)-ETHANONE'>PBP</scene> and <scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4]
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|GENE=
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}}
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'''PHOSPHOLIPASE A2 MODIFIED BY PBPB'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1BK9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gloydius_halys Gloydius halys] with <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=PBP:'>PBP</scene> and <scene name='pdbligand=BU1:'>BU1</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] Known structural/functional Site: <scene name='pdbsite=PBP:P-Bromo-Phenacyl-Bromide+Covalently+Binding+w.+Nd1+Of+HIS+48'>PBP</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BK9 OCA].
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1BK9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gloydius_halys Gloydius halys]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BK9 OCA].
==Reference==
==Reference==
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Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide., Zhao H, Tang L, Wang X, Zhou Y, Lin Z, Toxicon. 1998 Jun;36(6):875-86. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9663694 9663694]
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Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide., Zhao H, Tang L, Wang X, Zhou Y, Lin Z, Toxicon. 1998 Jun;36(6):875-86. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9663694 9663694]
[[Category: Gloydius halys]]
[[Category: Gloydius halys]]
[[Category: Phospholipase A(2)]]
[[Category: Phospholipase A(2)]]
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[[Category: platelet aggregation inhibitor]]
[[Category: platelet aggregation inhibitor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:56:14 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:12:09 2008''

Revision as of 08:12, 20 March 2008

Image:1bk9.jpg


PDB ID 1bk9

Drag the structure with the mouse to rotate
, resolution 2.00Å
Sites:
Ligands: , and
Activity: Phospholipase A(2), with EC number 3.1.1.4
Coordinates: save as pdb, mmCIF, xml



PHOSPHOLIPASE A2 MODIFIED BY PBPB


Overview

The crystal structure of acidic phospholipase A2 (APLA2) from Agkistrodon halys pallas covalently modified by p-bromo-phenacyl-bromide (pBPB) was determined to a resolution of 2.0 A by an isomorphous difference Fourier method with the native APLA2 structure as an initial model and refined to a crystallographic R factor of 15.3%. The modified APLA2 structure is remarkably similar to that of the native one. Least-squares superposition of C alpha atoms of native and modified APLA2 results in a root-mean-square coordinate deviation of 0.243 A. The p-bromo-phenacyl group near the active site occupies a position similar to that in pBPB modified bovine pancreatic PLA2. The inhibitor covalently bound to the NDI atom of His48 fits well in the hydrophobic channel, forming extensive hydrophobic interactions with the surrounding residues, especially with the side chains of Phe5 and Cys45 and the main chain of Gly30. However, the inhibitor does not change the conformation of these residues except that Trp31 at the entrance of the hydrophobic channel moves slightly toward the inhibitor. Compared with native APLA2, the Ca2+-binding loop shows a little conformational change and a cation, probably Na+, occupies in the position of Ca2+. The binding of pBPB to APLA2 induce no other significant conformational changes in the enzyme molecule elsewhere.

About this Structure

1BK9 is a Single protein structure of sequence from Gloydius halys. Full crystallographic information is available from OCA.

Reference

Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide., Zhao H, Tang L, Wang X, Zhou Y, Lin Z, Toxicon. 1998 Jun;36(6):875-86. PMID:9663694

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