2g58: Difference between revisions

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New page: left|200px<br /><applet load="2g58" size="450" color="white" frame="true" align="right" spinBox="true" caption="2g58, resolution 0.98Å" /> '''Crystal structure of...
 
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[[Image:2g58.gif|left|200px]]<br /><applet load="2g58" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2g58, resolution 0.98&Aring;" />
'''Crystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolution'''<br />


==About this Structure==
==Crystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolution==
2G58 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Daboia_russellii_pulchella Daboia russellii pulchella] with SO4 and PHQ 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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2G58 OCA].
<StructureSection load='2g58' size='340' side='right'caption='[[2g58]], [[Resolution|resolution]] 0.98&Aring;' scene=''>
[[Category: Daboia russellii pulchella]]
== Structural highlights ==
[[Category: Phospholipase A(2)]]
<table><tr><td colspan='2'>[[2g58]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Daboia_russelii_pulchella Daboia russelii pulchella]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G58 FirstGlance]. <br>
[[Category: Single protein]]
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.98&#8491;</td></tr>
[[Category: Betzel, C.]]
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PHQ:BENZYL+CHLOROCARBONATE'>PHQ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
[[Category: Dey, S.]]
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2g58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g58 OCA], [https://pdbe.org/2g58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g58 RCSB], [https://www.ebi.ac.uk/pdbsum/2g58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g58 ProSAT]</span></td></tr>
[[Category: Ethayathulla, A.S.]]
</table>
[[Category: Kaur, P.]]
== Function ==
[[Category: Kumar, R.Prem.]]
[https://www.uniprot.org/uniprot/PA2B8_DABRR PA2B8_DABRR] Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18062812</ref> <ref>PMID:2115497</ref> <ref>PMID:8835338</ref>
[[Category: Perbandt, M.]]
== Evolutionary Conservation ==
[[Category: Sharma, S.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Singh, N.]]
Check<jmol>
[[Category: Singh, T.P.]]
  <jmolCheckbox>
[[Category: Somvanshi, R.K.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g5/2g58_consurf.spt"</scriptWhenChecked>
[[Category: PHQ]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: SO4]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: 0.98 a resolution]]
  </jmolCheckbox>
[[Category: atomic resolution]]
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2g58 ConSurf].
[[Category: complex]]
<div style="clear:both"></div>
[[Category: crystal structure]]
[[Category: diars]]
[[Category: phospholipase a2]]


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:57:49 2007''
==See Also==
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Daboia russelii pulchella]]
[[Category: Large Structures]]
[[Category: Betzel C]]
[[Category: Dey S]]
[[Category: Ethayathulla AS]]
[[Category: Kaur P]]
[[Category: Perbandt M]]
[[Category: Prem Kumar R]]
[[Category: Sharma S]]
[[Category: Singh N]]
[[Category: Singh TP]]
[[Category: Somvanshi RK]]

Latest revision as of 11:47, 25 October 2023

Crystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolutionCrystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolution

Structural highlights

2g58 is a 2 chain structure with sequence from Daboia russelii pulchella. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 0.98Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PA2B8_DABRR Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.[1] [2] [3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Faure G, Gowda VT, Maroun RC. Characterization of a human coagulation factor Xa-binding site on Viperidae snake venom phospholipases A2 by affinity binding studies and molecular bioinformatics. BMC Struct Biol. 2007 Dec 6;7:82. PMID:18062812 doi:http://dx.doi.org/10.1186/1472-6807-7-82
  2. ↑ Kasturi S, Rudrammaji LM, Gowda TV. Antibodies to a phospholipase A2 from Vipera russelli selectively neutralize venom neurotoxicity. Immunology. 1990 Jun;70(2):175-80. PMID:2115497
  3. ↑ Tsai IH, Lu PJ, Su JC. Two types of Russell's viper revealed by variation in phospholipases A2 from venom of the subspecies. Toxicon. 1996 Jan;34(1):99-109. PMID:8835338

2g58, resolution 0.98Å

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