Proteopedia

1dtk: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(16 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1dtk.gif|left|200px]]


{{Structure
==THE NMR SOLUTION STRUCTURE OF DENDROTOXIN K FROM THE VENOM OF DENDROASPIS POLYLEPIS POLYLEPIS==
|PDB= 1dtk |SIZE=350|CAPTION= <scene name='initialview01'>1dtk</scene>
<StructureSection load='1dtk' size='340' side='right'caption='[[1dtk]]' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[1dtk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dendroaspis_polylepis_polylepis Dendroaspis polylepis polylepis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DTK FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</td></tr>
|GENE=  
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dtk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dtk OCA], [https://pdbe.org/1dtk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dtk RCSB], [https://www.ebi.ac.uk/pdbsum/1dtk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dtk ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dtk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dtk OCA], [http://www.ebi.ac.uk/pdbsum/1dtk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dtk RCSB]</span>
[https://www.uniprot.org/uniprot/VKTHK_DENPO VKTHK_DENPO] Serine protease inhibitor homolog that selectively blocks voltage-gated potassium channels homooligomer Kv1.1/KCNA1 (EC(50)=0.6 nM) and Kv1.1-containing heterooligomer.<ref>PMID:10429207</ref> <ref>PMID:8612784</ref> <ref>PMID:9134213</ref>
}}
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/1dtk_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1dtk ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The solution structure of dendrotoxin K (Toxin K), a protein consisting of one polypeptide chain with 57 residues purified from the venom of the black mamba, Dendroaspis polylepis polylepis, was determined by nuclear magnetic resonance (NMR) spectroscopy. On the basis of virtually complete sequence-specific 1H NMR assignments, including individual assignments for 38 pairs of diastereotopic substituents and side-chain amide protons, a total of 818 nuclear Overhauser effect distance constraints and 123 dihedral angle constraints were identified. Using this input, the solution structure of Toxin K was calculated with the program DIANA, and refined by restrained energy-minimization with a modified version of the program AMBER. The average root-mean-square deviation (r.m.s.d.) relative to the mean atomic co-ordinates of the 20 conformers selected to represent the solution structure is 0.31 A for all backbone atoms N, C alpha and C', and 0.90 A for all heavy-atoms of residues 2 to 56. The solution structure of Toxin K is very similar to the solution structure of the basic pancreatic trypsin inhibitor (BPTI) and the X-ray crystal structure of the alpha-dendrotoxin from Dendroaspis angusticeps (alpha-DTX), with r.m.s.d. values of 1.31 A and 0.92 A, respectively, for the backbone atoms of residues 2 to 56. Some local structural differences between Toxin K and BPTI are directly related to the fact that intermolecular interactions with two of the four internal molecules of hydration water in BPTI are replaced by intramolecular hydrogen bonds in Toxin K.


'''THE NMR SOLUTION STRUCTURE OF DENDROTOXIN K FROM THE VENOM OF DENDROASPIS POLYLEPIS POLYLEPIS'''
Nuclear magnetic resonance solution structure of dendrotoxin K from the venom of Dendroaspis polylepis polylepis.,Berndt KD, Guntert P, Wuthrich K J Mol Biol. 1993 Dec 5;234(3):735-50. PMID:8254670<ref>PMID:8254670</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dtk" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The solution structure of dendrotoxin K (Toxin K), a protein consisting of one polypeptide chain with 57 residues purified from the venom of the black mamba, Dendroaspis polylepis polylepis, was determined by nuclear magnetic resonance (NMR) spectroscopy. On the basis of virtually complete sequence-specific 1H NMR assignments, including individual assignments for 38 pairs of diastereotopic substituents and side-chain amide protons, a total of 818 nuclear Overhauser effect distance constraints and 123 dihedral angle constraints were identified. Using this input, the solution structure of Toxin K was calculated with the program DIANA, and refined by restrained energy-minimization with a modified version of the program AMBER. The average root-mean-square deviation (r.m.s.d.) relative to the mean atomic co-ordinates of the 20 conformers selected to represent the solution structure is 0.31 A for all backbone atoms N, C alpha and C', and 0.90 A for all heavy-atoms of residues 2 to 56. The solution structure of Toxin K is very similar to the solution structure of the basic pancreatic trypsin inhibitor (BPTI) and the X-ray crystal structure of the alpha-dendrotoxin from Dendroaspis angusticeps (alpha-DTX), with r.m.s.d. values of 1.31 A and 0.92 A, respectively, for the backbone atoms of residues 2 to 56. Some local structural differences between Toxin K and BPTI are directly related to the fact that intermolecular interactions with two of the four internal molecules of hydration water in BPTI are replaced by intramolecular hydrogen bonds in Toxin K.
*[[Dendrotoxin|Dendrotoxin]]
 
== References ==
==About this Structure==
<references/>
1DTK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Dendroaspis_polylepis_polylepis Dendroaspis polylepis polylepis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DTK OCA].
__TOC__
 
</StructureSection>
==Reference==
Nuclear magnetic resonance solution structure of dendrotoxin K from the venom of Dendroaspis polylepis polylepis., Berndt KD, Guntert P, Wuthrich K, J Mol Biol. 1993 Dec 5;234(3):735-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8254670 8254670]
[[Category: Dendroaspis polylepis polylepis]]
[[Category: Dendroaspis polylepis polylepis]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Berndt, K.]]
[[Category: Berndt K]]
[[Category: Guntert, P.]]
[[Category: Guntert P]]
[[Category: Wuthrich, K.]]
[[Category: Wuthrich K]]
[[Category: presynaptic neurotoxin]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:48:24 2008''

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/w/1dtk"