4kcf - Revision history

OCA at 15:57, 20 September 2023

2023-09-20T15:57:32Z

←Older revision		Revision as of 15:57, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kcf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomadura_kijaniata Actinomadura kijaniata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KCF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kcf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomadura_kijaniata Actinomadura kijaniata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KCF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKM:[(2R,4S,6R)-4-AZANYL-4,6-DIMETHYL-5,5-BIS(OXIDANYL)OXAN-2-YL]+[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AKM</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.098Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKM:[(2R,4S,6R)-4-AZANYL-4,6-DIMETHYL-5,5-BIS(OXIDANYL)OXAN-2-YL]+[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AKM</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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=4kcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcf OCA], [https://pdbe.org/4kcf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kcf RCSB], [https://www.ebi.ac.uk/pdbsum/4kcf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcf 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=4kcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcf OCA], [https://pdbe.org/4kcf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kcf RCSB], [https://www.ebi.ac.uk/pdbsum/4kcf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcf ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:52, 30 November 2022

2022-11-30T11:52:01Z

←Older revision		Revision as of 11:52, 30 November 2022
Line 1:		Line 1:

	==X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose==		==X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose==
-	<StructureSection load='4kcf' size='340' side='right' caption='[[4kcf]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='4kcf' size='340' side='right'caption='[[4kcf]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kcf]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_31588 Atcc 31588~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kcf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomadura_kijaniata Actinomadura kijaniata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KCF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKM:[(2R,4S,6R)-4-AZANYL-4,6-DIMETHYL-5,5-BIS(OXIDANYL)OXAN-2-YL]+[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AKM</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKM:[(2R,4S,6R)-4-AZANYL-4,6-DIMETHYL-5,5-BIS(OXIDANYL)OXAN-2-YL]+[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AKM</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3m9v\|3m9v]]</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=4kcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcf OCA], [https://pdbe.org/4kcf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kcf RCSB], [https://www.ebi.ac.uk/pdbsum/4kcf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcf ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KijD3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=46161 ATCC 31588])~~</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=4kcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcf OCA], [~~http~~://pdbe.org/4kcf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kcf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kcf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcf ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B3TMR1_ACTKI B3TMR1_ACTKI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 31588~~]]	+	[[Category: Actinomadura kijaniata]]
-	[[Category: ~~Branch, M C~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bruender, N A~~]]	+	[[Category: Branch MC]]
-	[[Category: ~~Holden, H M~~]]	+	[[Category: Bruender NA]]
-	[[Category: ~~Thoden, J B~~]]	+	[[Category: Holden HM]]
-	[[Category: ~~Zimmer, A L~~]]	+	[[Category: Thoden JB]]
-	[[Category: ~~6-trideoxy-4-keto-3-methyl-d-glucose]]~~	+	[[Category: Zimmer AL]]
-	~~[[Category: Class d flavin containing monooxygenase]]~~	+
-	~~[[Category: Dtdp-3-amino-2]]~~	+
-	~~[[Category: Fad]]~~	+
-	~~[[Category: Fatty acyl-coa dehydrogenase family]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Fmn]]~~	+
-	~~[[Category: Kijanimicin]]~~	+
-	~~[[Category: Kijanose]]~~	+
-	~~[[Category: Kijd3]]~~	+
-	~~[[Category: N-oxygenase]]~~	+
-	~~[[Category: Nucleotide linked sugar]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 19:00, 11 August 2016

2016-08-11T19:00:14Z

←Older revision		Revision as of 19:00, 11 August 2016
Line 1:		Line 1:
		+
	==X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose==		==X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose==
	<StructureSection load='4kcf' size='340' side='right' caption='[[4kcf]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4kcf' size='340' side='right' caption='[[4kcf]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3m9v\|3m9v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3m9v\|3m9v]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KijD3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=46161 ATCC 31588])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KijD3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=46161 ATCC 31588])</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=4kcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kcf RCSB], [http://www.ebi.ac.uk/pdbsum/4kcf 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=4kcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcf OCA], [http://pdbe.org/4kcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kcf RCSB], [http://www.ebi.ac.uk/pdbsum/4kcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4kcf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:58, 4 January 2015

2015-01-04T13:58:17Z

←Older revision		Revision as of 13:58, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4kcf\| PDB=4kcf \| SCENE= }}~~	+	==X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose==
-	===X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose===	+	<StructureSection load='4kcf' size='340' side='right' caption='[[4kcf]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23621882}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4kcf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_31588 Atcc 31588]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KCF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKM:[(2R,4S,6R)-4-AZANYL-4,6-DIMETHYL-5,5-BIS(OXIDANYL)OXAN-2-YL]+[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AKM</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3m9v\|3m9v]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KijD3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=46161 ATCC 31588])</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=4kcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kcf RCSB], [http://www.ebi.ac.uk/pdbsum/4kcf PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	KijD3 is a flavin-dependent N-oxygenase implicated in the formation of the nitro-containing sugar d-kijanose, found attached to the antibiotic kijanimicin. For this investigation, the structure of KijD3 in complex with FMN and its dTDP-sugar substrate was solved to 2.1 A resolution. In contrast to the apoenzyme structure, the C-terminus of the protein becomes ordered and projects into the active site cleft [Bruender, N. A., Thoden, J. B., and Holden, H. M. (2010) Biochemistry 49, 3517-3524]. The amino group of the dTDP-aminosugar that is oxidized is located 4.9 A from C4a of the flavin ring. The model provides a molecular basis for understanding the manner in which KijD3 catalyzes its unusual chemical transformation.

-	~~==About this Structure==~~	+	Active Site Architecture of a Sugar N-Oxygenase.,Thoden JB, Branch MC, Zimmer AL, Bruender NA, Holden HM Biochemistry. 2013 Apr 30. PMID:23621882<ref>PMID:23621882</ref>
-	~~[[4kcf]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Atcc_31588 Atcc 31588]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4KCF OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023621882</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Atcc 31588]]		[[Category: Atcc 31588]]
-	[[Category: Branch, M C.]]	+	[[Category: Branch, M C]]
-	[[Category: Bruender, N A.]]	+	[[Category: Bruender, N A]]
-	[[Category: Holden, H M.]]	+	[[Category: Holden, H M]]
-	[[Category: Thoden, J B.]]	+	[[Category: Thoden, J B]]
-	[[Category: Zimmer, A L.]]	+	[[Category: Zimmer, A L]]
	[[Category: 6-trideoxy-4-keto-3-methyl-d-glucose]]		[[Category: 6-trideoxy-4-keto-3-methyl-d-glucose]]
	[[Category: Class d flavin containing monooxygenase]]		[[Category: Class d flavin containing monooxygenase]]

OCA at 08:28, 18 December 2013

2013-12-18T08:28:05Z

←Older revision		Revision as of 08:28, 18 December 2013
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[4kcf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Actinomadura_kijaniata Actinomadura kijaniata~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCF OCA].	+	[[4kcf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_31588 Atcc 31588]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCF OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:023621882</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023621882</ref><references group="xtra"/><references/>
-	[[Category: ~~Actinomadura kijaniata~~]]	+	[[Category: Atcc 31588]]
	[[Category: Branch, M C.]]		[[Category: Branch, M C.]]
	[[Category: Bruender, N A.]]		[[Category: Bruender, N A.]]

OCA at 15:42, 19 June 2013

2013-06-19T15:42:12Z

←Older revision		Revision as of 15:42, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4kcf\| PDB=4kcf \| SCENE= }}
		+	===X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose===
		+	{{ABSTRACT_PUBMED_23621882}}

-	~~The entry~~ 4kcf is ~~ON HOLD~~	+	==About this Structure==
		+	[[4kcf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinomadura_kijaniata Actinomadura kijaniata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCF OCA].

-	~~Authors~~: Holden, H.M., Thoden, J.B.~~, Branch, M.C.,~~ Zimmer, A.L.~~, Bruender, N.A.~~	+	==Reference==
-		+	<ref group="xtra">PMID:023621882</ref><references group="xtra"/><references/>
-	~~Description~~: ~~X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,~~6-trideoxy-4-keto-3-methyl-D-glucose	+	[[Category: Actinomadura kijaniata]]
		+	[[Category: Branch, M C.]]
		+	[[Category: Bruender, N A.]]
		+	[[Category: Holden, H M.]]
		+	[[Category: Thoden, J B.]]
		+	[[Category: Zimmer, A L.]]
		+	[[Category: 6-trideoxy-4-keto-3-methyl-d-glucose]]
		+	[[Category: Class d flavin containing monooxygenase]]
		+	[[Category: Dtdp-3-amino-2]]
		+	[[Category: Fad]]
		+	[[Category: Fatty acyl-coa dehydrogenase family]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Fmn]]
		+	[[Category: Kijanimicin]]
		+	[[Category: Kijanose]]
		+	[[Category: Kijd3]]
		+	[[Category: N-oxygenase]]
		+	[[Category: Nucleotide linked sugar]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "4kcf" [edit=sysop:move=sysop]

2013-05-02T07:16:11Z

Protected "4kcf" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:16, 2 May 2013

OCA: New page: '''Unreleased structure''' The entry 4kcf is ON HOLD Authors: Holden, H.M., Thoden, J.B., Branch, M.C., Zimmer, A.L., Bruender, N.A. Description: X-ray Structure of a KijD3 in Complex ...

2013-05-02T07:16:10Z

New page: '''Unreleased structure''' The entry 4kcf is ON HOLD Authors: Holden, H.M., Thoden, J.B., Branch, M.C., Zimmer, A.L., Bruender, N.A. Description: X-ray Structure of a KijD3 in Complex ...

New page

'''Unreleased structure'''

The entry 4kcf is ON HOLD

Authors: Holden, H.M., Thoden, J.B., Branch, M.C., Zimmer, A.L., Bruender, N.A.

Description: X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose