+Open data
-Basic information
Entry | Database: PDB / ID: 1flt | ||||||
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Title | VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR | ||||||
Components |
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Keywords | COMPLEX (GROWTH FACTOR/TRANSFERASE) / COMPLEX (GROWTH FACTOR-TRANSFERASE) / FLT-1 RECEPTOR / CYSTINE KNOT / GLYCOPROTEIN / IMMUNOGLOBULIN-LIKE DOMAIN TRANSFERASE / COMPLEX (GROWTH FACTOR-TRANSFERASE) complex | ||||||
Function / homology | Function and homology information vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / 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-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / 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 / motor neuron migration / Neurophilin interactions with VEGF and VEGFR / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / 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 / vascular endothelial growth factor receptor activity / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / embryonic morphogenesis / camera-type eye morphogenesis / positive regulation of epithelial tube formation / negative regulation of cell-cell adhesion mediated by cadherin / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / positive regulation of vascular permeability / dopaminergic neuron differentiation / surfactant homeostasis / positive regulation of endothelial cell chemotaxis / platelet-derived growth factor receptor binding / extracellular matrix binding / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / artery morphogenesis / cardiac muscle cell development / sprouting angiogenesis / negative regulation of vascular endothelial cell proliferation / positive regulation of positive chemotaxis / blood vessel morphogenesis / Regulation of gene expression by Hypoxia-inducible Factor / vascular endothelial growth factor signaling pathway / positive regulation of leukocyte migration / positive regulation of p38MAPK cascade / 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 / activation of protein kinase activity / chemoattractant activity / growth factor binding / positive regulation of focal adhesion assembly / monocyte chemotaxis / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / positive regulation of cell division / macrophage differentiation / fibronectin binding / positive regulation of cell adhesion / positive regulation of blood vessel endothelial cell migration / mammary gland alveolus development / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / positive regulation of phospholipase C activity / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / extracellular matrix Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT/NCS AVERAGING / Resolution: 1.7 Å | ||||||
Authors | Wiesmann, C. / De Vos, A.M. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Crystal structure at 1.7 A resolution of VEGF in complex with domain 2 of the Flt-1 receptor. Authors: Wiesmann, C. / Fuh, G. / Christinger, H.W. / Eigenbrot, C. / Wells, J.A. / de Vos, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1flt.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1flt.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 1flt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/1flt ftp://data.pdbj.org/pub/pdb/validation_reports/fl/1flt | HTTPS FTP |
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-Related structure data
Related structure data | 1vpfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 11511.249 Da / Num. of mol.: 2 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15692 #2: Protein | Mass: 10906.662 Da / Num. of mol.: 2 Fragment: SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P17948, receptor protein-tyrosine kinase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Feb 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 47047 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.052 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.27 / % possible all: 95.8 |
Reflection | *PLUS Num. measured all: 332877 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 95.8 % / Num. unique obs: 4520 / Rmerge(I) obs: 0.277 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT/NCS AVERAGING Starting model: 1VPF Resolution: 1.7→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2
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Displacement parameters | Biso mean: 31.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.32 |