1BK9

PHOSPHOLIPASE A2 MODIFIED BY PBPB

Summary for 1BK9

• Entry DOI: 10.2210/pdb1bk9/pdb
• Descriptor: PHOSPHOLIPASE A2, CALCIUM ION, p-Bromophenacyl bromide, ... (5 entities in total)
• Functional Keywords: hydrolase, phospholipase a2, platelet aggregation inhibitor, pbpb
• Biological source: Gloydius halys (halys viper)
• Total number of polymer chains: 1
• Total formula weight: 14396.95

Authors

Zhao, H.,Tang, L.,Wang, X.,Lin, Z.,Zhou, Y. (deposition date: 1998-07-16, release date: 1999-03-02, Last modification date: 2024-10-09)

Primary citation

Zhao, H.,Tang, L.,Wang, X.,Zhou, Y.,Lin, Z.
Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide.
Toxicon, 36:875-886, 1998

PubMed Abstract: 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.

PubMed: 9663694
DOI: 10.1016/S0041-0101(97)00169-4

Experimental method

X-RAY DIFFRACTION (2 Å)