5k64 - Revision history

OCA at 10:41, 27 September 2023

OCA — Wed, 27 Sep 2023 10:41:34 GMT

←Older revision		Revision as of 10:41, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5k64' size='340' side='right'caption='[[5k64]], [[Resolution\|resolution]] 2.44Å' scene=''>		<StructureSection load='5k64' size='340' side='right'caption='[[5k64]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k64]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K64 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K64 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k64]] 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=5K64 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K64 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.44Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5k64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k64 OCA], [~~http~~://pdbe.org/5k64 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k64 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k64 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k64 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5k64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k64 OCA], [https://pdbe.org/5k64 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k64 RCSB], [https://www.ebi.ac.uk/pdbsum/5k64 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k64 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[~~http~~://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.	+	[https://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[https://omim.org/entry/254500 254500]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Djinovic-Carugo, K]]	+	[[Category: Djinovic-Carugo K]]
-	[[Category: Humm, A]]	+	[[Category: Humm A]]
-	[[Category: Kitzmuller, M]]	+	[[Category: Kitzmuller M]]
-	[[Category: Lobner, E]]	+	[[Category: Lobner E]]
-	[[Category: Mlynek, G]]	+	[[Category: Mlynek G]]
-	[[Category: Obinger, C]]	+	[[Category: Obinger C]]
-	~~[[Category: Antibody engineering]]~~	+
-	~~[[Category: Ch3 domain]]~~	+
-	~~[[Category: Fc fragment]]~~	+
-	~~[[Category: Fcab]]~~	+
-	~~[[Category: Glycosylation]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin g1]]~~	+
-	~~[[Category: Vascular endothelial growth factor]]~~	+
-	~~[[Category: Vegf~~]]	+

OCA at 09:22, 25 June 2020

OCA — Thu, 25 Jun 2020 09:22:16 GMT

←Older revision		Revision as of 09:22, 25 June 2020
Line 1:		Line 1:

	==Crystal structure of VEGF binding IgG1-Fc (Fcab 448)==		==Crystal structure of VEGF binding IgG1-Fc (Fcab 448)==
-	<StructureSection load='5k64' size='340' side='right' caption='[[5k64]], [[Resolution\|resolution]] 2.44Å' scene=''>	+	<StructureSection load='5k64' size='340' side='right'caption='[[5k64]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k64]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K64 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K64 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k64]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K64 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K64 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=5k64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k64 OCA], [http://pdbe.org/5k64 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k64 RCSB], [http://www.ebi.ac.uk/pdbsum/5k64 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k64 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k64 OCA], [http://pdbe.org/5k64 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k64 RCSB], [http://www.ebi.ac.uk/pdbsum/5k64 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k64 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Djinovic-Carugo, K]]		[[Category: Djinovic-Carugo, K]]
	[[Category: Humm, A]]		[[Category: Humm, A]]

OCA at 03:42, 6 September 2017

OCA — Wed, 06 Sep 2017 03:42:56 GMT

←Older revision		Revision as of 03:42, 6 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k64 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of VEGF binding IgG1-Fc (Fcab 448)==
		+	<StructureSection load='5k64' size='340' side='right' caption='[[5k64]], [[Resolution\|resolution]] 2.44Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k64]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K64 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K64 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=5k64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k64 OCA], [http://pdbe.org/5k64 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k64 RCSB], [http://www.ebi.ac.uk/pdbsum/5k64 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k64 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[http://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Fcabs (Fc domain with antigen-binding sites) are promising novel therapeutics. By engineering of the C-terminal loops of the CH3 domains, two antigen binding sites can be inserted in close proximity. In order to elucidate the binding mode(s) between homodimeric Fcabs and small homodimeric antigens, the interaction between the Fcabs 448 and CT6 (having the AB, CD and EF loops and the C-termini engineered) with homodimeric VEGF was investigated. The crystal structures of these Fcabs, which form polymers with the antigen VEGF in solution, were determined. However, construction of heterodimeric Fcabs (JanusFcabs: one chain Fc-wt, one chain VEGF-binding) results in formation of distinct JanusFcab-VEGF complexes (2:1), which allowed elucidation of the crystal structure of the JanusCT6-VEGF complex at 2.15 A resolution. VEGF binding to Janus448 and JanusCT6 is shown to be entropically unfavorable, but enthalpically favorable. Structure-function relationships are discussed with respect to Fcab design and engineering strategies.

-	~~Authors~~:	+	Two-Faced Fcab Prevents Polymerization with VEGF and Reveals Thermodynamics and the 2.15 A Crystal Structure of the Complex.,Lobner E, Humm AS, Mlynek G, Kubinger K, Kitzmuller M, Traxlmayr MW, Djinovic-Carugo K, Obinger C MAbs. 2017 Aug 17:0. doi: 10.1080/19420862.2017.1364825. PMID:28816592<ref>PMID:28816592</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5k64" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Djinovic-Carugo, K]]
		+	[[Category: Humm, A]]
		+	[[Category: Kitzmuller, M]]
		+	[[Category: Lobner, E]]
		+	[[Category: Mlynek, G]]
		+	[[Category: Obinger, C]]
		+	[[Category: Antibody engineering]]
		+	[[Category: Ch3 domain]]
		+	[[Category: Fc fragment]]
		+	[[Category: Fcab]]
		+	[[Category: Glycosylation]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin g1]]
		+	[[Category: Vascular endothelial growth factor]]
		+	[[Category: Vegf]]

OCA at 13:48, 9 September 2016

OCA — Fri, 09 Sep 2016 13:48:51 GMT

←Older revision		Revision as of 13:48, 9 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k64 is ON HOLD	+	The entry 5k64 is ON HOLD until Paper Publication

-	Authors: ~~Humm, A., Lobner, E., Kitzmuller, M., Mlynek, G., Obinger, C., Djinovic-Carugo, K.~~	+	Authors:

-	Description: ~~Crystal structure of VEGF binding IgG1-Fc (Fcab 448)~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Djinovic-Carugo, K]]
-	[[Category: Mlynek, G]]
-	[[Category: Lobner, E]]
-	[[Category: Humm, A]]
-	[[Category: Obinger, C]]
-	[[Category: Kitzmuller, M]]

OCA: Protected "5k64" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:22:35 GMT

Protected "5k64" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:22, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k64 is ON HOLD Authors: Humm, A., Lobner, E., Kitzmuller, M., Mlynek, G., Obinger, C., Djinovic-Carugo, K. Description: Crystal structure of VEGF ...

OCA — Wed, 01 Jun 2016 14:22:34 GMT

New page: '''Unreleased structure''' The entry 5k64 is ON HOLD Authors: Humm, A., Lobner, E., Kitzmuller, M., Mlynek, G., Obinger, C., Djinovic-Carugo, K. Description: Crystal structure of VEGF ...

New page

'''Unreleased structure'''

The entry 5k64 is ON HOLD

Authors: Humm, A., Lobner, E., Kitzmuller, M., Mlynek, G., Obinger, C., Djinovic-Carugo, K.

Description: Crystal structure of VEGF binding IgG1-Fc (Fcab 448)
[[Category: Unreleased Structures]]
[[Category: Djinovic-Carugo, K]]
[[Category: Mlynek, G]]
[[Category: Lobner, E]]
[[Category: Humm, A]]
[[Category: Obinger, C]]
[[Category: Kitzmuller, M]]