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Yorodumi- PDB-1vgh: HEPARIN-BINDING DOMAIN FROM VASCULAR ENDOTHELIAL GROWTH FACTOR, N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vgh | ||||||
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Title | HEPARIN-BINDING DOMAIN FROM VASCULAR ENDOTHELIAL GROWTH FACTOR, NMR, 20 STRUCTURES | ||||||
Components | VASCULAR ENDOTHELIAL GROWTH FACTOR-165 | ||||||
Keywords | GROWTH FACTOR / HEPARIN-BINDING / ANGIOGENESIS | ||||||
Function / homology | Function and homology information basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis ...basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / positive regulation of peptidyl-tyrosine autophosphorylation / negative regulation of adherens junction organization / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / 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 / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / motor neuron migration / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / eye photoreceptor cell development / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / positive regulation of axon extension involved in axon guidance / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of protein localization to early endosome / vascular wound healing / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / camera-type eye morphogenesis / positive regulation of epithelial tube formation / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / dopaminergic neuron differentiation / positive regulation of vascular permeability / surfactant homeostasis / positive regulation of endothelial cell chemotaxis / platelet-derived growth factor receptor binding / cell migration involved in sprouting angiogenesis / extracellular matrix binding / retinal ganglion cell axon guidance / cardiac muscle cell development / sprouting angiogenesis / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / vascular endothelial growth factor signaling pathway / positive regulation of leukocyte migration / positive regulation of p38MAPK cascade / artery morphogenesis / positive regulation of DNA biosynthetic process / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / chemoattractant activity / activation of protein kinase activity / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / positive regulation of cell division / macrophage differentiation / fibronectin binding / positive regulation of cell adhesion / mammary gland alveolus development / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell proliferation / extracellular matrix / positive regulation of endothelial cell migration / negative regulation of miRNA transcription / platelet alpha granule lumen / VEGFR2 mediated cell proliferation / secretory granule / kidney development / cytokine activity / positive regulation of epithelial cell proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS | ||||||
Authors | Fairbrother, W.J. / Champe, M.A. / Christinger, H.W. / Keyt, B.A. / Starovasnik, M.A. | ||||||
Citation | 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vgh.cif.gz | 342.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vgh.ent.gz | 298.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/1vgh ftp://data.pdbj.org/pub/pdb/validation_reports/vg/1vgh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 5.5 / Temperature: 300 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST RESIDUAL RESTRAINT VIOLATION ENERGIES Conformers calculated total number: 50 / Conformers submitted total number: 20 |