1ppm - Revision history

OCA at 05:57, 17 April 2024

OCA — Wed, 17 Apr 2024 05:57:53 GMT

←Older revision		Revision as of 05:57, 17 April 2024
Line 3:		Line 3:
	<StructureSection load='1ppm' size='340' side='right'caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1ppm' size='340' side='right'caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Cbs_340.48 Cbs 340.48~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_janthinellum Penicillium janthinellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ppl\|1ppl]], [[1ppk\|1ppk]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [https://pdbe.org/1ppm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [https://www.ebi.ac.uk/pdbsum/1ppm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppm 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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [https://pdbe.org/1ppm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [https://www.ebi.ac.uk/pdbsum/1ppm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PEPA1_PENJA PEPA1_PENJA] Secreted aspartic endopeptidase that allows assimilation of proteinaceous substrates. The scissile peptide bond is attacked by a nucleophilic water molecule activated by two aspartic residues in the active site. Shows a broad primary substrate specificity. Favors hydrophobic residues at the P1 and P1' positions, but can also activate trypsinogen and hydrolyze the B chain of insulin between positions 'Gly-20' and 'Glu-21'.<ref>PMID:4946839</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=1ppm 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=1ppm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The molecular structures of three phosphorus-based peptide inhibitors of aspartyl proteinases complexed with penicillopepsin [1, Iva-L-Val-L-Val-StaPOEt [Iva = isovaleryl, StaP = the phosphinic acid analogue of statine [(S)-4-amino-(S)-3-hydroxy-6-methylheptanoic acid] (IvaVVStaPOEt)]; 2, Iva-L-Val-L-Val-L-LeuP-(O)Phe-OMe [LeuP = the phosphinic acid analogue of L-leucine; (O)Phe = L-3-phenyllactic acid; OMe = methyl ester] [Iva VVLP(O)FOMe]; and 3, Cbz-L-Ala-L-Ala-L-LeuP-(O)-Phe-OMe (Cbz = benzyloxycarbonyl) [CbzAALP(O)FOMe]] have been determined by X-ray crystallography and refined to crystallographic agreement factors, R ( = sigma parallel to F0 magnitude of - Fc parallel to/sigma magnitude of F0), of 0.132, 0.131, and 0.134, respectively. These inhibitors were designed to be structural mimics of the tetrahederal transition-state intermediate encountered during aspartic proteinase catalysis. They are potent inhibitors of penicillopepsin with Ki values of 1, 22 nM; 2, 2.8 nM; and 3, 1600 nM, respectively [Bartlett, P. A., Hanson, J. E., & Giannousis, P. P. (1990) J. Org. Chem. 55, 6268-6274]. All three of these phosphorus-based inhibitors bind virtually identically in the active site of penicillopepsin in a manner that closely approximates that expected for the transition state [James, M. N. G., Sielecki, A.R., Hayakawa, K., & Gelb, M. H. (1992) Biochemistry 31, 3872-3886]. The pro-S oxygen atom of the two phosphonate inhibitors and of the phosphinate group of the StaP inhibitor make very short contact distances (approximately 2.4 A) to the carboxyl oxygen atom, O delta 1, of Asp33 on penicillopepsin. We have interpreted this distance and the stereochemical environment of the carboxyl and phosphonate groups in terms of a hydrogen bond that most probably has a symmetric single-well potential energy function. The pro-R oxygen atom is the recipient of a hydrogen bond from the carboxyl group of Asp213. Thus, we are able to assign a neutral status to Asp213 and a partially negatively charged status to Asp33 with reasonable confidence. Similar very short hydrogen bonds involving the active site glutamic acid residues of thermolysin and carboxypeptidase A and the pro-R oxygen of bound phosphonate inhibitors have been reported [Holden, H. M., Tronrud, D. E., Monzingo, A. F., Weaver, L. H., & Matthews, B. W. (1987) Biochemistry 26, 8542-8553; Kim, H., & Lipscomb, W. N. (1991) Biochemistry 30, 8171-8180].(ABSTRACT TRUNCATED AT 400 WORDS)
-
-	Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues.,Fraser ME, Strynadka NC, Bartlett PA, Hanson JE, James MN Biochemistry. 1992 Jun 9;31(22):5201-14. PMID:1606144<ref>PMID:1606144</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ppm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cbs 340 48]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Penicillopepsin~~]]	+	[[Category: Penicillium janthinellum]]
-	[[Category: Fraser~~, M E~~]]	+	[[Category: Fraser ME]]
-	[[Category: James~~, M N.G]]~~	+	[[Category: James MNG]]
-	~~[[Category: Acid proteinase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 10:48, 19 May 2021

OCA — Wed, 19 May 2021 10:48:09 GMT

←Older revision		Revision as of 10:48, 19 May 2021
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	<StructureSection load='1ppm' size='340' side='right'caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1ppm' size='340' side='right'caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cbs_340.48 Cbs 340.48]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cbs_340.48 Cbs 340.48]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ppl\|1ppl]], [[1ppk\|1ppk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ppl\|1ppl]], [[1ppk\|1ppk]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [~~http~~://pdbe.org/1ppm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ppm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppm 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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [https://pdbe.org/1ppm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [https://www.ebi.ac.uk/pdbsum/1ppm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 10:59, 17 July 2019

OCA — Wed, 17 Jul 2019 10:59:38 GMT

←Older revision		Revision as of 10:59, 17 July 2019
Line 1:		Line 1:

	==CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES==		==CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES==
-	<StructureSection load='1ppm' size='340' side='right' caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1ppm' size='340' side='right'caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_340.48 Cbs 340.48]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_340.48 Cbs 340.48]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPM FirstGlance]. <br>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1ppm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ppm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Penicillopepsin\|Penicillopepsin]]
		+	*[[Pepsin\|Pepsin]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Cbs 340 48]]		[[Category: Cbs 340 48]]
		+	[[Category: Large Structures]]
	[[Category: Penicillopepsin]]		[[Category: Penicillopepsin]]
	[[Category: Fraser, M E]]		[[Category: Fraser, M E]]

OCA at 07:57, 24 February 2018

OCA — Sat, 24 Feb 2018 07:57:26 GMT

←Older revision		Revision as of 07:57, 24 February 2018
Line 1:		Line 1:
		+
	==CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES==		==CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES==
	<StructureSection load='1ppm' size='340' side='right' caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1ppm' size='340' side='right' caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Penja Penja~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_340.48 Cbs 340.48]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ppl\|1ppl]], [[1ppk\|1ppk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ppl\|1ppl]], [[1ppk\|1ppk]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [http://pdbe.org/1ppm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [http://www.ebi.ac.uk/pdbsum/1ppm 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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [http://pdbe.org/1ppm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [http://www.ebi.ac.uk/pdbsum/1ppm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/1ppm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/1ppm_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>
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1ppm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ppm" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Penicillopepsin\|Penicillopepsin]]
-	*[[Pepsin\|Pepsin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cbs 340 48]]
	[[Category: Penicillopepsin]]		[[Category: Penicillopepsin]]
-	[[Category: Penja]]
	[[Category: Fraser, M E]]		[[Category: Fraser, M E]]
	[[Category: James, M N.G]]		[[Category: James, M N.G]]
	[[Category: Acid proteinase]]		[[Category: Acid proteinase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 04:16, 7 February 2016

OCA — Sun, 07 Feb 2016 04:16:57 GMT

←Older revision		Revision as of 04:16, 7 February 2016
Line 16:		Line 16:
	<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=1ppm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:44, 9 September 2015

OCA — Wed, 09 Sep 2015 21:44:51 GMT

←Older revision		Revision as of 21:44, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1ppm' size='340' side='right' caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1ppm' size='340' side='right' caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Penicillium_janthinellum Penicillium janthinellum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penja Penja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ppl\|1ppl]], [[1ppk\|1ppk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ppl\|1ppl]], [[1ppk\|1ppk]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [http://www.ebi.ac.uk/pdbsum/1ppm 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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [http://pdbe.org/1ppm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [http://www.ebi.ac.uk/pdbsum/1ppm PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1ppm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Penicillium janthinellum]]
	[[Category: Penicillopepsin]]		[[Category: Penicillopepsin]]
		+	[[Category: Penja]]
	[[Category: Fraser, M E]]		[[Category: Fraser, M E]]
	[[Category: James, M N.G]]		[[Category: James, M N.G]]
	[[Category: Acid proteinase]]		[[Category: Acid proteinase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 07:47, 6 January 2015

OCA — Tue, 06 Jan 2015 07:47:05 GMT

←Older revision		Revision as of 07:47, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_janthinellum Penicillium janthinellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_janthinellum Penicillium janthinellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ppl\|1ppl]], [[1ppk\|1ppk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ppl\|1ppl]], [[1ppk\|1ppk]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </span></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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [http://www.ebi.ac.uk/pdbsum/1ppm 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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [http://www.ebi.ac.uk/pdbsum/1ppm PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Penicillium janthinellum]]		[[Category: Penicillium janthinellum]]
	[[Category: Penicillopepsin]]		[[Category: Penicillopepsin]]
-	[[Category: Fraser, M E.]]	+	[[Category: Fraser, M E]]
-	[[Category: James, M N.G.]]	+	[[Category: James, M N.G]]
	[[Category: Acid proteinase]]		[[Category: Acid proteinase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 20:09, 28 September 2014

OCA — Sun, 28 Sep 2014 20:09:12 GMT

←Older revision		Revision as of 20:09, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ppm.~~png~~\|~~left~~\|200px]]	+	==CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES==
		+	<StructureSection load='1ppm' size='340' side='right' caption='[[1ppm]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_janthinellum Penicillium janthinellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0P1:N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N-{(1S)-1-[(R)-[(1R)-1-BENZYL-2-METHOXY-2-OXOETHOXY](HYDROXY)PHOSPHORYL]-3-METHYLBUTYL}-L-ALANINAMIDE'>0P1</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ppl\|1ppl]], [[1ppk\|1ppk]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Penicillopepsin Penicillopepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.20 3.4.23.20] </span></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=1ppm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppm RCSB], [http://www.ebi.ac.uk/pdbsum/1ppm PDBsum]</span></td></tr>
		+	<table>
		+	== 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/pp/1ppm_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 ==
		+	The molecular structures of three phosphorus-based peptide inhibitors of aspartyl proteinases complexed with penicillopepsin [1, Iva-L-Val-L-Val-StaPOEt [Iva = isovaleryl, StaP = the phosphinic acid analogue of statine [(S)-4-amino-(S)-3-hydroxy-6-methylheptanoic acid] (IvaVVStaPOEt)]; 2, Iva-L-Val-L-Val-L-LeuP-(O)Phe-OMe [LeuP = the phosphinic acid analogue of L-leucine; (O)Phe = L-3-phenyllactic acid; OMe = methyl ester] [Iva VVLP(O)FOMe]; and 3, Cbz-L-Ala-L-Ala-L-LeuP-(O)-Phe-OMe (Cbz = benzyloxycarbonyl) [CbzAALP(O)FOMe]] have been determined by X-ray crystallography and refined to crystallographic agreement factors, R ( = sigma parallel to F0 magnitude of - Fc parallel to/sigma magnitude of F0), of 0.132, 0.131, and 0.134, respectively. These inhibitors were designed to be structural mimics of the tetrahederal transition-state intermediate encountered during aspartic proteinase catalysis. They are potent inhibitors of penicillopepsin with Ki values of 1, 22 nM; 2, 2.8 nM; and 3, 1600 nM, respectively [Bartlett, P. A., Hanson, J. E., & Giannousis, P. P. (1990) J. Org. Chem. 55, 6268-6274]. All three of these phosphorus-based inhibitors bind virtually identically in the active site of penicillopepsin in a manner that closely approximates that expected for the transition state [James, M. N. G., Sielecki, A.R., Hayakawa, K., & Gelb, M. H. (1992) Biochemistry 31, 3872-3886]. The pro-S oxygen atom of the two phosphonate inhibitors and of the phosphinate group of the StaP inhibitor make very short contact distances (approximately 2.4 A) to the carboxyl oxygen atom, O delta 1, of Asp33 on penicillopepsin. We have interpreted this distance and the stereochemical environment of the carboxyl and phosphonate groups in terms of a hydrogen bond that most probably has a symmetric single-well potential energy function. The pro-R oxygen atom is the recipient of a hydrogen bond from the carboxyl group of Asp213. Thus, we are able to assign a neutral status to Asp213 and a partially negatively charged status to Asp33 with reasonable confidence. Similar very short hydrogen bonds involving the active site glutamic acid residues of thermolysin and carboxypeptidase A and the pro-R oxygen of bound phosphonate inhibitors have been reported [Holden, H. M., Tronrud, D. E., Monzingo, A. F., Weaver, L. H., & Matthews, B. W. (1987) Biochemistry 26, 8542-8553; Kim, H., & Lipscomb, W. N. (1991) Biochemistry 30, 8171-8180].(ABSTRACT TRUNCATED AT 400 WORDS)

-	~~{{STRUCTURE_1ppm\| PDB=1ppm \| SCENE= }}~~	+	Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues.,Fraser ME, Strynadka NC, Bartlett PA, Hanson JE, James MN Biochemistry. 1992 Jun 9;31(22):5201-14. PMID:1606144<ref>PMID:1606144</ref>

-	~~===CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_1606144}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ppm]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Penicillium_janthinellum Penicillium janthinellum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA].~~	+

	==See Also==		==See Also==
	*[[Penicillopepsin\|Penicillopepsin]]		*[[Penicillopepsin\|Penicillopepsin]]
	*[[Pepsin\|Pepsin]]		*[[Pepsin\|Pepsin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:001606144<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Penicillium janthinellum]]		[[Category: Penicillium janthinellum]]
	[[Category: Penicillopepsin]]		[[Category: Penicillopepsin]]

OCA at 05:33, 20 October 2012

OCA — Sat, 20 Oct 2012 05:33:37 GMT

←Older revision		Revision as of 05:33, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ppm]] is a 1 chain structure ~~of [[Penicillopepsin]] and [[Pepsin]]~~ with sequence from [http://en.wikipedia.org/wiki/Penicillium_janthinellum Penicillium janthinellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA].	+	[[1ppm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_janthinellum Penicillium janthinellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPM OCA].

	==See Also==		==See Also==

OCA: Protected "1ppm" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 10:27:38 GMT

Protected "1ppm" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:27, 25 July 2012