6m8y - Revision history

OCA at 06:26, 11 October 2023

OCA — Wed, 11 Oct 2023 06:26:30 GMT

←Older revision		Revision as of 06:26, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6m8y' size='340' side='right'caption='[[6m8y]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='6m8y' size='340' side='right'caption='[[6m8y]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m8y]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Achromobacter_parvulus_t1 Achromobacter parvulus t1~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kdy 1kdy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M8Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6M8Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m8y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._101 Pseudomonas sp. 101] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kdy 1kdy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M8Y FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</scene~~>, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=~~PHL~~:~~L-PHENYLALANINOL~~'>~~PHL~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PHL:L-PHENYLALANINOL'>PHL</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat">pcp ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33067 Achromobacter parvulus T1])</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=6m8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m8y OCA], [https://pdbe.org/6m8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m8y RCSB], [https://www.ebi.ac.uk/pdbsum/6m8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m8y ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Sedolisin Sedolisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.100 3.4.21.100]~~ </~~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=6m8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m8y OCA], [~~http~~://pdbe.org/6m8y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6m8y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6m8y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6m8y ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PICP_PSESR PICP_PSESR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
	*[[Pepsin\|Pepsin]]		*[[Pepsin\|Pepsin]]
-	*[[Proteinase\|Proteinase]]	+	*[[Proteinase 3D structures\|Proteinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Achromobacter parvulus t1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sedolisin~~]]	+	[[Category: Pseudomonas sp. 101]]
-	[[Category: Dauter, Z]]	+	[[Category: Synthetic construct]]
-	[[Category: Dunn~~, B M~~]]	+	[[Category: Dauter Z]]
-	[[Category: Goldfarb~~, N E~~]]	+	[[Category: Dunn BM]]
-	[[Category: Gustchina, A]]	+	[[Category: Goldfarb NE]]
-	[[Category: Li, M]]	+	[[Category: Gustchina A]]
-	[[Category: Oda, K]]	+	[[Category: Li M]]
-	[[Category: Oyama, H]]	+	[[Category: Oda K]]
-	[[Category: Uchida, K]]	+	[[Category: Oyama H]]
-	[[Category: Wlodawer, A]]	+	[[Category: Uchida K]]
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+	[[Category: Wlodawer A]]
-	~~[[Category: Serine-carboxyl proteinase~~]]	+

OCA at 10:20, 4 December 2019

OCA — Wed, 04 Dec 2019 10:20:51 GMT

←Older revision		Revision as of 10:20, 4 December 2019
Line 1:		Line 1:

	==PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR AIPF==		==PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR AIPF==
-	<StructureSection load='6m8y' size='340' side='right' caption='[[6m8y]], [[Resolution\|resolution]] 1.10Å' scene=''>	+	<StructureSection load='6m8y' size='340' side='right'caption='[[6m8y]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m8y]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kdy 1kdy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M8Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m8y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_parvulus_t1 Achromobacter parvulus t1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kdy 1kdy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M8Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=PHL:L-PHENYLALANINOL'>PHL</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=PHL:L-PHENYLALANINOL'>PHL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pcp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33067 Achromobacter parvulus T1])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sedolisin Sedolisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.100 3.4.21.100] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sedolisin Sedolisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.100 3.4.21.100] </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=6m8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m8y OCA], [http://pdbe.org/6m8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m8y RCSB], [http://www.ebi.ac.uk/pdbsum/6m8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m8y 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=6m8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m8y OCA], [http://pdbe.org/6m8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m8y RCSB], [http://www.ebi.ac.uk/pdbsum/6m8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m8y ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 6m8y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6m8y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pepsin\|Pepsin]]
		+	*[[Proteinase\|Proteinase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Achromobacter parvulus t1]]
		+	[[Category: Large Structures]]
	[[Category: Sedolisin]]		[[Category: Sedolisin]]
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]

OCA at 05:40, 24 October 2018

OCA — Wed, 24 Oct 2018 05:40:50 GMT

←Older revision		Revision as of 05:40, 24 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The~~ entry 6m8y is ~~ON HOLD~~	+	==PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR AIPF==
		+	<StructureSection load='6m8y' size='340' side='right' caption='[[6m8y]], [[Resolution\|resolution]] 1.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6m8y]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kdy 1kdy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M8Y FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=PHL:L-PHENYLALANINOL'>PHL</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sedolisin Sedolisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.100 3.4.21.100] </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=6m8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m8y OCA], [http://pdbe.org/6m8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m8y RCSB], [http://www.ebi.ac.uk/pdbsum/6m8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m8y ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystal structures of the serine-carboxyl proteinase from Pseudomonas sp. 101 (PSCP), complexed with a number of inhibitors, have been solved and refined at high- to atomic-level resolution. All of these inhibitors (tyrostatin, pseudo-tyrostatin, AcIPF, AcIAF, and chymostatin, as well as previously studied iodotyrostatin and pseudo-iodotyrostatin) make covalent bonds to the active site Ser287 through their aldehyde moieties, while their side chains occupy subsites S1-S4 of the enzyme. The mode of binding of the inhibitors is almost identical for their P1 and P2 side chains, while significant differences are observed for P3 and P4 (if present). Kinetic parameters for the binding of these nanomolar inhibitors to PSCP have been established and correlated with the observed mode of binding. The preferences of this enzyme for a larger side chain in P2 as well as Tyr or Phe in P1 are explained by the size, shape, and characteristics of the S2 and S1 regions of the protein structure, respectively. Networks of hydrogen bonds involving glutamic and aspartic acids have been analyzed for the atomic-resolution structure of the native enzyme. PSCP contains a calcium-binding site that consists of Asp328, Asp348, three amide carbonyl groups, and a water molecule, in almost perfect octahedral coordination. The presence of Ca(2+) cation is necessary for the activity of the enzyme.

-	~~Authors: Wlodawer~~, A., Li, M., Gustchina, A., Dauter, Z., Uchida, K., Oyama, H., Goldfarb~~, N.E.~~, Dunn~~, B.M.~~, Oda, K.	+	Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase.,Wlodawer A, Li M, Gustchina A, Dauter Z, Uchida K, Oyama H, Goldfarb NE, Dunn BM, Oda K Biochemistry. 2001 Dec 25;40(51):15602-11. PMID:11747435<ref>PMID:11747435</ref>

-	~~Description: PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR AIPF~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Dunn, B.M~~]]	+	<div class="pdbe-citations 6m8y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Sedolisin]]
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]
-	[[Category: ~~Oda~~, K]]	+	[[Category: Dunn, B M]]
-	[[Category: Goldfarb, N.E]]	+	[[Category: Goldfarb, N E]]
-	~~[[Category: Wlodawer, A]]~~	+
-	~~[[Category: Oyama, H~~]]	+
	[[Category: Gustchina, A]]		[[Category: Gustchina, A]]
	[[Category: Li, M]]		[[Category: Li, M]]
		+	[[Category: Oda, K]]
		+	[[Category: Oyama, H]]
	[[Category: Uchida, K]]		[[Category: Uchida, K]]
		+	[[Category: Wlodawer, A]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Serine-carboxyl proteinase]]

OCA at 06:11, 12 September 2018

OCA — Wed, 12 Sep 2018 06:11:06 GMT

←Older revision		Revision as of 06:11, 12 September 2018
Line 5:		Line 5:
	Authors: Wlodawer, A., Li, M., Gustchina, A., Dauter, Z., Uchida, K., Oyama, H., Goldfarb, N.E., Dunn, B.M., Oda, K.		Authors: Wlodawer, A., Li, M., Gustchina, A., Dauter, Z., Uchida, K., Oyama, H., Goldfarb, N.E., Dunn, B.M., Oda, K.

-	Description: ~~Inhibitor complexes of the Pseudomonas serine~~-~~carboxyl proteinase~~	+	Description: PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR AIPF
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Dunn, B.M]]		[[Category: Dunn, B.M]]

OCA: Protected "6m8y" [edit=sysop:move=sysop]

OCA — Wed, 29 Aug 2018 06:08:26 GMT

Protected "6m8y" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:08, 29 August 2018

OCA: New page: '''Unreleased structure''' The entry 6m8y is ON HOLD Authors: Wlodawer, A., Li, M., Gustchina, A., Dauter, Z., Uchida, K., Oyama, H., Goldfarb, N.E., Dunn, B.M., Oda, K. Description: I...

OCA — Wed, 29 Aug 2018 06:08:25 GMT

New page: '''Unreleased structure''' The entry 6m8y is ON HOLD Authors: Wlodawer, A., Li, M., Gustchina, A., Dauter, Z., Uchida, K., Oyama, H., Goldfarb, N.E., Dunn, B.M., Oda, K. Description: I...

New page

'''Unreleased structure'''

The entry 6m8y is ON HOLD

Authors: Wlodawer, A., Li, M., Gustchina, A., Dauter, Z., Uchida, K., Oyama, H., Goldfarb, N.E., Dunn, B.M., Oda, K.

Description: Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase
[[Category: Unreleased Structures]]
[[Category: Dunn, B.M]]
[[Category: Dauter, Z]]
[[Category: Oda, K]]
[[Category: Goldfarb, N.E]]
[[Category: Wlodawer, A]]
[[Category: Oyama, H]]
[[Category: Gustchina, A]]
[[Category: Li, M]]
[[Category: Uchida, K]]