1dpy
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1dpy |SIZE=350|CAPTION= <scene name='initialview01'>1dpy</scene>, resolution 2.45Å | |PDB= 1dpy |SIZE=350|CAPTION= <scene name='initialview01'>1dpy</scene>, resolution 2.45Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene> | + | |LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> |
| - | |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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dpy OCA], [http://www.ebi.ac.uk/pdbsum/1dpy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dpy RCSB]</span> | ||
}} | }} | ||
| Line 29: | Line 32: | ||
[[Category: Singh, T P.]] | [[Category: Singh, T P.]] | ||
[[Category: Srinivasan, A.]] | [[Category: Srinivasan, A.]] | ||
| - | [[Category: NA]] | ||
[[Category: crystal structure]] | [[Category: crystal structure]] | ||
[[Category: indian common krait venom]] | [[Category: indian common krait venom]] | ||
| Line 35: | Line 37: | ||
[[Category: refinement]] | [[Category: refinement]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:46:27 2008'' |
Revision as of 16:46, 30 March 2008
| |||||||
| , resolution 2.45Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Phospholipase A(2), with EC number 3.1.1.4 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THREE-DIMENSIONAL STRUCTURE OF A NOVEL PHOSPHOLIPASE A2 FROM INDIAN COMMON KRAIT AT 2.45 A RESOLUTION
Overview
This is the first phospholipase A2 (PLA2) structure from the family of kraits. The protein was isolated from Bungarus caeruleus (common krait) and the primary sequence was determined using cDNA approach. Three-dimensional structure of this presynaptic neurotoxic PLA2 from group I has been determined by molecular replacement method using the model of PLA2 component of beta2-bungarotoxin (Bungarus multicinctus) and refined using CNS package to a final R-factor of 20.1 % for all the data in resolution range 20.0-2.4 A. The final refined model comprises 897 protein atoms and 77 water molecules. The overall framework of krait phospholipase A2 with three long helices and two short antiparallel beta-strands is extremely similar to those observed for other group I PLA2s. However, the critical parts of PLA2 folding are concerned with its various functional loops. The conformations of these loops determine the efficiency of enzyme action and presence/absence of various pharmacological functions. In the present structure calcium-binding loop is occupied by a sodium ion with a 7-fold co-ordination. The conformation of loop 55-75 in krait PLA2 corresponds to a very high activity of the enzyme. A comparison of its sequence with multimeric PLA2s clearly shows the absence of critical residues such as Tyr3, Trp61 and Phe64, which are involved in the multimerization of PLA2 molecules. The protein shows anticoagulant and neurotoxic activities.
About this Structure
1DPY is a Single protein structure of sequence from Bungarus caeruleus. Full crystallographic information is available from OCA.
Reference
Sequence and crystal structure determination of a basic phospholipase A2 from common krait (Bungarus caeruleus) at 2.4 A resolution: identification and characterization of its pharmacological sites., Singh G, Gourinath S, Sharma S, Paramasivam M, Srinivasan A, Singh TP, J Mol Biol. 2001 Apr 6;307(4):1049-59. PMID:11286555
Page seeded by OCA on Sun Mar 30 19:46:27 2008
