2pm5: Difference between revisions

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==Human alpha-defensin 1 derivative (HNP1)==
==Human alpha-defensin 1 derivative (HNP1)==
<StructureSection load='2pm5' size='340' side='right' caption='[[2pm5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='2pm5' size='340' side='right'caption='[[2pm5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2pm5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PM5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PM5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2pm5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PM5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DEFA1, DEF1, DEFA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pm5 OCA], [https://pdbe.org/2pm5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pm5 RCSB], [https://www.ebi.ac.uk/pdbsum/2pm5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pm5 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pm5 OCA], [http://pdbe.org/2pm5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pm5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pm5 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DEF3_HUMAN DEF3_HUMAN] Defensin 2 and defensin 3 have antibiotic, fungicide and antiviral activities. Has antimicrobial activity against Gram-negative and Gram-positive bacteria. Defensins are thought to kill microbes by permeabilizing their plasma membrane.<ref>PMID:15616305</ref> <ref>PMID:2006422</ref> <ref>PMID:15894545</ref> <ref>PMID:17452329</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pm/2pm5_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pm/2pm5_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
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==See Also==
==See Also==
*[[Defensin|Defensin]]
*[[Defensin 3D structures|Defensin 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Lu, W]]
[[Category: Large Structures]]
[[Category: Lubkowski, J]]
[[Category: Lu W]]
[[Category: Pazgier, M]]
[[Category: Lubkowski J]]
[[Category: Antimicrobial]]
[[Category: Pazgier M]]
[[Category: Antimicrobial protein]]
[[Category: Defensin]]
[[Category: Derivative]]

Latest revision as of 14:04, 30 August 2023

Human alpha-defensin 1 derivative (HNP1)Human alpha-defensin 1 derivative (HNP1)

Structural highlights

2pm5 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DEF3_HUMAN Defensin 2 and defensin 3 have antibiotic, fungicide and antiviral activities. Has antimicrobial activity against Gram-negative and Gram-positive bacteria. Defensins are thought to kill microbes by permeabilizing their plasma membrane.[1] [2] [3] [4]

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. ↑ Ericksen B, Wu Z, Lu W, Lehrer RI. Antibacterial activity and specificity of the six human {alpha}-defensins. Antimicrob Agents Chemother. 2005 Jan;49(1):269-75. PMID:15616305 doi:10.1128/AAC.49.1.269-275.2005
  2. ↑ Hill CP, Yee J, Selsted ME, Eisenberg D. Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization. Science. 1991 Mar 22;251(5000):1481-5. PMID:2006422
  3. ↑ Xie C, Prahl A, Ericksen B, Wu Z, Zeng P, Li X, Lu WY, Lubkowski J, Lu W. Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids. J Biol Chem. 2005 Sep 23;280(38):32921-9. Epub 2005 May 13. PMID:15894545 doi:M503084200
  4. ↑ Zou G, de Leeuw E, Li C, Pazgier M, Li C, Zeng P, Lu WY, Lubkowski J, Lu W. Toward understanding the cationicity of defensins. Arg and Lys versus their noncoded analogs. J Biol Chem. 2007 Jul 6;282(27):19653-65. Epub 2007 Apr 23. PMID:17452329 doi:10.1074/jbc.M611003200

2pm5, resolution 2.40Å

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OCA
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