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- PDB-2xac: Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Reco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xac | ||||||
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Title | Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity | ||||||
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![]() | TRANSFERASE/SIGNALING PROTEIN / TRANSFERASE-SIGNALING PROTEIN COMPLEX / ANGIOGENESIS / CYSTEINE-KNOT PROTEIN / MITOGEN / TRANSFERASE / SIGNALING PROTEIN | ||||||
Function / homology | ![]() vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / positive regulation of vascular wound healing / hyaloid vascular plexus regression / vascular endothelial growth factor receptor 1 binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / positive regulation of vascular wound healing / hyaloid vascular plexus regression / vascular endothelial growth factor receptor 1 binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / induction of positive chemotaxis / vascular endothelial growth factor receptor 2 binding / coronary vasculature development / protein O-linked glycosylation / positive regulation of vascular endothelial growth factor receptor signaling pathway / sprouting angiogenesis / negative regulation of vascular endothelial cell proliferation / blood vessel morphogenesis / vascular endothelial growth factor signaling pathway / chemoattractant activity / growth factor binding / monocyte chemotaxis / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / : / cardiac muscle contraction / positive regulation of endothelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / platelet alpha granule lumen / growth factor activity / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / actin cytoskeleton / Platelet degranulation / heparin binding / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / cell differentiation / receptor complex / response to hypoxia / endosome / positive regulation of cell migration / positive regulation of protein phosphorylation / negative regulation of gene expression / focal adhesion / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Iyer, S. / Darley, P. / Acharya, K.R. | ||||||
![]() | ![]() Title: Structural Insights Into the Binding of Vegf-B by Vegfr-1D2: Recognition and Specificity Authors: Iyer, S. / Darley, P. / Acharya, K.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.2 KB | Display | ![]() |
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PDB format | ![]() | 65.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.5 KB | Display | ![]() |
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Full document | ![]() | 472 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11157.050 Da / Num. of mol.: 2 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 31-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11209.933 Da / Num. of mol.: 2 / Fragment: DOMAIN 2, RESIDUES 129-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17948, receptor protein-tyrosine kinase #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % / Description: NONE |
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Crystal grow | pH: 8 Details: 14% PEG 4000, 0.1M SODIUM CITRATE, PH 5.6 AND 0.2M LICL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→40 Å / Num. obs: 11510 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.71→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.6 / % possible all: 47.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2C7W AND 1FLT Resolution: 2.71→32.76 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.801 / SU B: 25.128 / SU ML: 0.519 / Cross valid method: THROUGHOUT / ESU R Free: 0.606 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→32.76 Å
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