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- PDB-1kmx: Heparin-binding Domain from Vascular Endothelial Growth Factor -

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Basic information

Entry
Database: PDB / ID: 1kmx
TitleHeparin-binding Domain from Vascular Endothelial Growth Factor
Componentsvascular endothelial growth factor
KeywordsHORMONE/GROWTH FACTOR / heparin-binding / angiogenesis / growth factor / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / lymph vessel morphogenesis / primitive erythrocyte differentiation / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / VEGF-activated neuropilin signaling pathway / bone trabecula formation / coronary vein morphogenesis / lung vasculature development / cardiac vascular smooth muscle cell development / lymphangiogenesis / endothelial cell chemotaxis / positive regulation of trophoblast cell migration / vascular endothelial growth factor receptor-2 signaling pathway / positive regulation of epithelial tube formation / VEGF binds to VEGFR leading to receptor dimerization / motor neuron migration / regulation of nitric oxide mediated signal transduction / positive regulation of protein localization to early endosome / eye photoreceptor cell development / positive regulation of axon extension involved in axon guidance / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / camera-type eye morphogenesis / positive regulation of branching involved in ureteric bud morphogenesis / neuropilin binding / coronary artery morphogenesis / induction of positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / vascular endothelial growth factor receptor 2 binding / negative regulation of cell-cell adhesion mediated by cadherin / commissural neuron axon guidance / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of vascular permeability / positive regulation of blood vessel branching / platelet-derived growth factor receptor binding / surfactant homeostasis / cell migration involved in sprouting angiogenesis / endothelial cell proliferation / extracellular matrix binding / epithelial cell maturation / positive regulation of leukocyte migration / positive regulation of positive chemotaxis / cardiac muscle cell development / sprouting angiogenesis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of endothelial cell chemotaxis / vascular endothelial growth factor signaling pathway / artery morphogenesis / negative regulation of epithelial to mesenchymal transition / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / negative regulation of fat cell differentiation / positive chemotaxis / positive regulation of sprouting angiogenesis / chemoattractant activity / mesoderm development / outflow tract morphogenesis / positive regulation of protein autophosphorylation / monocyte differentiation / fibronectin binding / macrophage differentiation / positive regulation of cell division / positive regulation of receptor internalization / neuroblast proliferation / mammary gland alveolus development / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / heart morphogenesis / cell maturation / ovarian follicle development / homeostasis of number of cells within a tissue / positive regulation of endothelial cell proliferation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / positive regulation of endothelial cell migration
Similarity search - Function
Vascular Endothelial Growth Factor-165, Heparin-binding Domain / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. ...Vascular Endothelial Growth Factor-165, Heparin-binding Domain / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsStauffer, M.E. / Skelton, N.J. / Fairbrother, W.J.
Citation
Journal: J.BIOMOL.NMR / Year: 2002
Title: Refinement of the Solution Structure of the Heparin-binding Domain of Vascular Endothelial Growth Factor using Residual Dipolar Couplings
Authors: Stauffer, M.E. / Skelton, N.J. / Fairbrother, W.J.
#1: Journal: Structure / Year: 1998
Title: Solution Structure of the Heparin-binding Domain of Vascular endothelial Growth Factor
Authors: Fairbrother, W.J. / Champe, M.A. / Christinger, H.W. / Keyt, B.A. / Starovasnik, M.A.
History
DepositionDec 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 9, 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: vascular endothelial growth factor


Theoretical massNumber of molelcules
Total (without water)6,4961
Polymers6,4961
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)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein vascular endothelial growth factor


Mass: 6496.479 Da / Num. of mol.: 1 / Fragment: heparin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15692
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
2323D 15N-separated NOESY
242HNHA
353DQF-COSY
3632D NOESY
2722D 15N IPAP-HSQC
4842D 15N IPAP HSQC
NMR detailsText: The structure was refined using 1H-15N dipolar coupling restraints

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0 mM VEGF heparin-binding domain; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide90% H2O/10% D2O
22.0 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide90% H2O/10% D2O
32.0 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide99.9% D2O
40.6 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride; 0.02% sodium azide4:1:0.2 ditridecanoyl-phosphatidylcholine/dihexanoyl-phosphatidylcholine/cetyltrimethylammonium bromide, 5% w/v total lipid in 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125 mM sodium acetate; 50 mM sodium chloride 5.5ambient 300 K
225 mM sodium acetate; 50 mM sodium chloride 5.5ambient 300 K
325 mM sodium acetate; 50 mM sodium chloride 5.5ambient 300 K
425 mM sodium acetate; 50 mM sodium chloride 5.5ambient 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameDeveloperClassification
UXNMRcollection
XwinNMRcollection
Felixprocessing
Felixdata analysis
CNXstructure solution
CNXMolecular Simulations, Inc.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on 459 NOE-derived distance restraints, 28 H-bond restraints, 66 dihedral angle restraints, and 38 residual dipolar coupling restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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