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- PDB-1qsz: THE VEGF-BINDING DOMAIN OF FLT-1 (MINIMIZED MEAN) -

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Entry
Database: PDB / ID: 1qsz
TitleTHE VEGF-BINDING DOMAIN OF FLT-1 (MINIMIZED MEAN)
ComponentsVASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / IMMUNOGLOBULIN-LIKE DOMAIN / I-SET / VEGF RECEPTOR / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / negative regulation of vascular endothelial cell proliferation / blood vessel morphogenesis / monocyte chemotaxis ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / negative regulation of vascular endothelial cell proliferation / blood vessel morphogenesis / monocyte chemotaxis / growth factor binding / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / cell migration / actin cytoskeleton / angiogenesis / protein autophosphorylation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / receptor complex / endosome / positive regulation of cell migration / focal adhesion / positive regulation of cell population proliferation / extracellular space / ATP binding / plasma membrane
Similarity search - Function
Vascular endothelial growth factor receptor 1 (VEGFR1) / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain ...Vascular endothelial growth factor receptor 1 (VEGFR1) / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING; MOLECULAR DYNAMICS
Model type detailsminimized average
AuthorsStarovasnik, M.A. / Christinger, H.W. / Wiesmann, C. / Champe, M.A. / de Vos, A.M. / Skelton, N.J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Solution structure of the VEGF-binding domain of Flt-1: comparison of its free and bound states.
Authors: Starovasnik, M.A. / Christinger, H.W. / Wiesmann, C. / Champe, M.A. / de Vos, A.M. / Skelton, N.J.
History
DepositionJun 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Assembly

Deposited unit
A: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)11,5381
Polymers11,5381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1 / FLT-1


Mass: 11538.298 Da / Num. of mol.: 1 / Fragment: SECOND EXTRACELLULAR IMMUNOGLOBULIN-LIKE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: MODIFIED QIAGEN PQE30 CONTAINING HIS-TAG AND GENENASE CLEAVAGE SITE
Production host: Escherichia coli (E. coli) / References: UniProt: P17948
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1223D 15N-SEPARATED NOESY
132HNHA
142HNHB
1523D 15N SEPARATED TOCSY (32 AND 96 MS)
1623D 15N SEPARATED ROESY (40MS)
NMR detailsText: AN ADDITIONAL SAMPLE THAT WAS 15% 13C LABELED WAS USED TO OBTAIN STEREOSPECIFIC ASSIGNMENTS OF PROCHIRAL METHYL GROUPS.

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Sample preparation

Details
Solution-IDContents
11MM FLT-1(DOMAIN2) U-15N,13C; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS
21MM FLT-1(DOMAIN2) U-15N; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS
31MM FLT-1(DOMAIN2) 15% 13C; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS
Sample conditionsIonic strength: 150mM / pH: 5.7 / Pressure: AMBIENT / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR910901BRUKERcollection
Felix97MOLECULAR SIMULATIONS, INC.processing
Felix97MOLECULAR SIMULATIONS, INC.data analysis
DGII95MOLECULAR SIMULATIONS, INC.structure solution
Discover95MOLECULAR SIMULATIONS, INC.refinement
Discover95MOLECULAR SIMULATIONS, INC.structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING; MOLECULAR DYNAMICS
Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 2054 NOE-DERIVED DISTANCE RESTRAINTS, 122 DIHEDRAL RESTRAINTS, AND 44 DISTANCE RESTRAINTS FROM HYDROGEN BONDS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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