2bdg - Revision history

OCA at 06:24, 3 April 2024

2024-04-03T06:24:08Z

← Older revision		Revision as of 06:24, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='2bdg' size='340' side='right'caption='[[2bdg]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2bdg' size='340' side='right'caption='[[2bdg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bdg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BDG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bdg]] 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=2BDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BDG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</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]] 1.95Å</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene></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=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [https://pdbe.org/2bdg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [https://www.ebi.ac.uk/pdbsum/2bdg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bdg ProSAT]</span></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=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [https://pdbe.org/2bdg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [https://www.ebi.ac.uk/pdbsum/2bdg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bdg ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[https://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Defects in KLK4 are the cause of amelogenesis imperfecta hypomaturation type 2A1 (AI2A1) [MIM:[https://omim.org/entry/204700 204700]]. AI2A1 is an autosomal recessive defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel.<ref>PMID:15235027</ref>		[https://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN] Defects in KLK4 are the cause of amelogenesis imperfecta hypomaturation type 2A1 (AI2A1) [MIM:[https://omim.org/entry/204700 204700]. AI2A1 is an autosomal recessive defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel.<ref>PMID:15235027</ref>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Involved in enamel formation.<ref>PMID:15235027</ref>		[https://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN] Involved in enamel formation.<ref>PMID:15235027</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2bdg ConSurf].		</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=2bdg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Human tissue kallikrein 4 (hK4) belongs to a 15-member family of closely related serine proteinases. hK4 is predominantly expressed in prostate, activates hK3/PSA, and is up-regulated in prostate and ovarian cancer. We have identified active monomers of recombinant hK4 besides inactive oligomers in solution. hK4 crystallised in the presence of zinc, nickel, and cobalt ions in three crystal forms containing cyclic tetramers and octamers. These structures display a novel metal site between His25 and Glu77 that links the 70-80 loop with the N-terminal segment. Micromolar zinc as present in prostatic fluid inhibits the enzymatic activity of hK4 against fluorogenic substrates. In our measurements, wild-type hK4 exhibited a zinc inhibition constant (IC50) of 16 microM including a permanent residual activity, in contrast to the zinc-independent mutants H25A and E77A. Since the Ile16 N terminus of wild-type hK4 becomes more accessible for acetylating agents in the presence of zinc, we propose that zinc affects the hK4 active site via the salt-bridge formed between the N terminus and Asp194 required for a functional active site. hK4 possesses an unusual 99-loop that creates a groove-like acidic S2 subsite. These findings explain the observed specificity of hK4 for the P1 to P4 substrate residues. Moreover, hK4 shows a negatively charged surface patch, which may represent an exosite for prime-side substrate recognition.

	Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site.,Debela M, Magdolen V, Grimminger V, Sommerhoff C, Messerschmidt A, Huber R, Friedrich R, Bode W, Goettig P J Mol Biol. 2006 Oct 6;362(5):1094-107. Epub 2006 Aug 3. PMID:16950394<ref>PMID:16950394</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2bdg" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
Line 38:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bode, W]]		[[Category: Bode W]]
	[[Category: Debela, M]]		[[Category: Debela M]]
	[[Category: Goettig, P]]		[[Category: Goettig P]]
	~~[[Category: SPINE, Structural Proteomics in Europe]]~~
	~~[[Category: 70-80 loop]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: S1 subsite]]~~
	~~[[Category: Serine proteinase]]~~
	~~[[Category: Spine]]~~
	~~[[Category: Structural genomic]]~~
	~~[[Category: Structural proteomics in europe~~]]

OCA at 11:40, 3 February 2021

2021-02-03T11:40:12Z

← Older revision		Revision as of 11:40, 3 February 2021
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	==Human Kallikrein 4 complex with nickel and p-aminobenzamidine==		==Human Kallikrein 4 complex with nickel and p-aminobenzamidine==
	<StructureSection load='2bdg' size='340' side='right' caption='[[2bdg]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2bdg' size='340' side='right'caption='[[2bdg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bdg]] 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=2BDG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2BDG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bdg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BDG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([https://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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [~~http~~://pdbe.org/2bdg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2bdg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2bdg ProSAT]</span></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=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [https://pdbe.org/2bdg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [https://www.ebi.ac.uk/pdbsum/2bdg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bdg ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[~~http~~://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Defects in KLK4 are the cause of amelogenesis imperfecta hypomaturation type 2A1 (AI2A1) [MIM:[~~http~~://omim.org/entry/204700 204700]]. AI2A1 is an autosomal recessive defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel.<ref>PMID:15235027</ref>		[[https://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Defects in KLK4 are the cause of amelogenesis imperfecta hypomaturation type 2A1 (AI2A1) [MIM:[https://omim.org/entry/204700 204700]]. AI2A1 is an autosomal recessive defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel.<ref>PMID:15235027</ref>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Involved in enamel formation.<ref>PMID:15235027</ref>		[[https://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Involved in enamel formation.<ref>PMID:15235027</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==See Also==		==See Also==
	*[[Kallikrein\|Kallikrein]]		*[[Kallikrein 3D structures\|Kallikrein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Bode, W]]		[[Category: Bode, W]]
	[[Category: Debela, M]]		[[Category: Debela, M]]

OCA at 06:53, 16 May 2018

2018-05-16T06:53:15Z

← Older revision		Revision as of 06:53, 16 May 2018
Line 1:		Line 1:

	==Human Kallikrein 4 complex with nickel and p-aminobenzamidine==		==Human Kallikrein 4 complex with nickel and p-aminobenzamidine==
	<StructureSection load='2bdg' size='340' side='right' caption='[[2bdg]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2bdg' size='340' side='right' caption='[[2bdg]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [http://pdbe.org/2bdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [http://www.ebi.ac.uk/pdbsum/2bdg PDBsum]</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=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [http://pdbe.org/2bdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [http://www.ebi.ac.uk/pdbsum/2bdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2bdg ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bd/2bdg_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bd/2bdg_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>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</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=2bdg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:06, 11 September 2015

2015-09-11T08:06:49Z

← Older revision		Revision as of 08:06, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2bdg' size='340' side='right' caption='[[2bdg]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2bdg' size='340' side='right' caption='[[2bdg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bdg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BDG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bdg]] 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=2BDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BDG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [http://www.ebi.ac.uk/pdbsum/2bdg PDBsum]</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=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [http://pdbe.org/2bdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [http://www.ebi.ac.uk/pdbsum/2bdg PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2bdg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Bode, W]]		[[Category: Bode, W]]
	[[Category: Debela, M]]		[[Category: Debela, M]]

OCA at 09:48, 8 January 2015

2015-01-08T09:48:04Z

← Older revision		Revision as of 09:48, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bdg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BDG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bdg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BDG FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [http://www.ebi.ac.uk/pdbsum/2bdg PDBsum]</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=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [http://www.ebi.ac.uk/pdbsum/2bdg PDBsum]</span></td></tr>
	<table>		</table>
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Defects in KLK4 are the cause of amelogenesis imperfecta hypomaturation type 2A1 (AI2A1) [MIM:[http://omim.org/entry/204700 204700]]. AI2A1 is an autosomal recessive defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel.<ref>PMID:15235027</ref>		[[http://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Defects in KLK4 are the cause of amelogenesis imperfecta hypomaturation type 2A1 (AI2A1) [MIM:[http://omim.org/entry/204700 204700]]. AI2A1 is an autosomal recessive defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel.<ref>PMID:15235027</ref>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bode, W.]]		[[Category: Bode, W]]
	[[Category: Debela, M.]]		[[Category: Debela, M]]
	[[Category: Goettig, P.]]		[[Category: Goettig, P]]
	[[Category: SPINE, Structural Proteomics in Europe.]]		[[Category: SPINE, Structural Proteomics in Europe]]
	[[Category: 70-80 loop]]		[[Category: 70-80 loop]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 00:33, 30 September 2014

2014-09-30T00:33:59Z

← Older revision		Revision as of 00:33, 30 September 2014
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	~~{{STRUCTURE_2bdg~~\| ~~PDB~~=2bdg \| ~~SCENE~~= }}		==Human Kallikrein 4 complex with nickel and p-aminobenzamidine==
	===~~Human Kallikrein 4 complex with nickel~~ and p-~~aminobenzamidine~~===		<StructureSection load='2bdg' size='340' side='right' caption='[[2bdg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	~~{{ABSTRACT_PUBMED_16950394}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2bdg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BDG FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene><br>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLK4, EMSP1, PRSS17, PSTS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bdg RCSB], [http://www.ebi.ac.uk/pdbsum/2bdg PDBsum]</span></td></tr>
			<table>
			== Disease ==
			[[http://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Defects in KLK4 are the cause of amelogenesis imperfecta hypomaturation type 2A1 (AI2A1) [MIM:[http://omim.org/entry/204700 204700]]. AI2A1 is an autosomal recessive defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel.<ref>PMID:15235027</ref>
			== Function ==
			[[http://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Involved in enamel formation.<ref>PMID:15235027</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/bd/2bdg_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Human tissue kallikrein 4 (hK4) belongs to a 15-member family of closely related serine proteinases. hK4 is predominantly expressed in prostate, activates hK3/PSA, and is up-regulated in prostate and ovarian cancer. We have identified active monomers of recombinant hK4 besides inactive oligomers in solution. hK4 crystallised in the presence of zinc, nickel, and cobalt ions in three crystal forms containing cyclic tetramers and octamers. These structures display a novel metal site between His25 and Glu77 that links the 70-80 loop with the N-terminal segment. Micromolar zinc as present in prostatic fluid inhibits the enzymatic activity of hK4 against fluorogenic substrates. In our measurements, wild-type hK4 exhibited a zinc inhibition constant (IC50) of 16 microM including a permanent residual activity, in contrast to the zinc-independent mutants H25A and E77A. Since the Ile16 N terminus of wild-type hK4 becomes more accessible for acetylating agents in the presence of zinc, we propose that zinc affects the hK4 active site via the salt-bridge formed between the N terminus and Asp194 required for a functional active site. hK4 possesses an unusual 99-loop that creates a groove-like acidic S2 subsite. These findings explain the observed specificity of hK4 for the P1 to P4 substrate residues. Moreover, hK4 shows a negatively charged surface patch, which may represent an exosite for prime-side substrate recognition.

	~~==Disease==~~		Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site.,Debela M, Magdolen V, Grimminger V, Sommerhoff C, Messerschmidt A, Huber R, Friedrich R, Bode W, Goettig P J Mol Biol. 2006 Oct 6;362(5):1094-107. Epub 2006 Aug 3. PMID:16950394<ref>PMID:16950394</ref>
	~~[[http~~:~~//www~~.~~uniprot~~.~~org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Defects in KLK4 are the cause of amelogenesis imperfecta hypomaturation type 2A1~~ (~~AI2A1~~) ~~[MIM~~:~~[http://omim~~.org/entry/204700 204700]]. AI2A1 is an autosomal recessive defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel.<ref>PMID:~~15235027~~</ref>

	~~==Function==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[http:~~/~~/www~~.~~uniprot~~.~~org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Involved in enamel formation~~.<~~ref~~>~~PMID:15235027~~</~~ref~~>		</div>

	==~~About this Structure~~==		==See Also==
	[[~~2bdg~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDG OCA].		*[[Kallikrein\|Kallikrein]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:016950394</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bode, W.]]		[[Category: Bode, W.]]

OCA at 04:05, 25 March 2013

2013-03-25T04:05:16Z

← Older revision		Revision as of 04:05, 25 March 2013
Line 1:		Line 1:
	~~[[Image:2bdg.png\|left\|200px]]~~

	{{STRUCTURE_2bdg\| PDB=2bdg \| SCENE= }}		{{STRUCTURE_2bdg\| PDB=2bdg \| SCENE= }}
			===Human Kallikrein 4 complex with nickel and p-aminobenzamidine===
			{{ABSTRACT_PUBMED_16950394}}

	===~~Human Kallikrein 4 complex with nickel~~ and ~~p-aminobenzamidine===~~		==Disease==
			[[http://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Defects in KLK4 are the cause of amelogenesis imperfecta hypomaturation type 2A1 (AI2A1) [MIM:[http://omim.org/entry/204700 204700]]. AI2A1 is an autosomal recessive defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel.<ref>PMID:15235027</ref>

	~~{{ABSTRACT_PUBMED_16950394}}~~		==Function==
			[[http://www.uniprot.org/uniprot/KLK4_HUMAN KLK4_HUMAN]] Involved in enamel formation.<ref>PMID:15235027</ref>

	==About this Structure==		==About this Structure==
Line 11:		Line 13:

	==Reference==		==Reference==
	<ref group="xtra">PMID:016950394</ref><references group="xtra"/>		<ref group="xtra">PMID:016950394</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bode, W.]]		[[Category: Bode, W.]]

OCA: Protected "2bdg" [edit=sysop:move=sysop]

2013-01-06T09:56:23Z

Protected "2bdg" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:56, 6 January 2013
(No difference)

OCA at 09:56, 6 January 2013

2013-01-06T09:56:19Z

← Older revision		Revision as of 09:56, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2bdg.png\|left\|200px]]		[[Image:2bdg.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2bdg", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2bdg\| PDB=2bdg \| SCENE= }}		{{STRUCTURE_2bdg\| PDB=2bdg \| SCENE= }}

	===Human Kallikrein 4 complex with nickel and p-aminobenzamidine===		===Human Kallikrein 4 complex with nickel and p-aminobenzamidine===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16950394}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16950394 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16950394}}		{{ABSTRACT_PUBMED_16950394}}

	==About this Structure==		==About this Structure==
	~~2BDG~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDG OCA].		[[2bdg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDG OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16950394~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016950394</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bode, W.]]		[[Category: Bode, W.]]
Line 36:		Line 24:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Structural proteomics in europe]]		[[Category: Structural proteomics in europe]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:38:01 2009''~~

OCA at 15:38, 17 February 2009

2009-02-17T15:38:03Z

← Older revision		Revision as of 15:38, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
	Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site., Debela M, Magdolen V, Grimminger V, Sommerhoff C, Messerschmidt A, Huber R, Friedrich R, Bode W, Goettig P, J Mol Biol. 2006 Oct 6;362(5):1094-107. Epub 2006 Aug 3. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~16950394 16950394]~~		<ref group="xtra">PMID:16950394</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bode, W.]]		[[Category: Bode, W.]]
Line 37:		Line 37:
	[[Category: Structural proteomics in europe]]		[[Category: Structural proteomics in europe]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Dec 10 15~~:47:~~56 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:38:01 2009''