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Open data
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Basic information
Entry | Database: PDB / ID: 6mk0 | ||||||||||||
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Title | Integrin AlphaVBeta3 ectodomain bound to antagonist TDI-4161 | ||||||||||||
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![]() | CELL ADHESION / HYBRID DOMAIN / PSI / EGF REPEATS / BETA TAIL / CALF / THIGH / BETA PROPELLER / RGD MOTIF / FIBRONECTIN / VITRONECTIN | ||||||||||||
Function / homology | ![]() integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding ...integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / Laminin interactions / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / entry into host cell by a symbiont-containing vacuole / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / regulation of phagocytosis / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / platelet-derived growth factor receptor binding / filopodium membrane / positive regulation of small GTPase mediated signal transduction / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / positive regulation of intracellular signal transduction / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus / smooth muscle cell migration / microvillus membrane / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / endodermal cell differentiation / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / platelet-derived growth factor receptor signaling pathway / negative regulation of lipid storage / fibronectin binding / positive regulation of cell adhesion / ECM proteoglycans / voltage-gated calcium channel activity / positive regulation of T cell migration / positive regulation of bone resorption / vasculogenesis / Integrin cell surface interactions / coreceptor activity / specific granule membrane / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / extrinsic apoptotic signaling pathway in absence of ligand / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / ERK1 and ERK2 cascade / embryo implantation / phagocytic vesicle / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | van Agthoven, J. / Arnaout, M.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Novel Pure alphaVbeta3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations Authors: Li, J. / Fukase, Y. / Shang, Y. / Zou, W. / Munoz-Felix, J. / Buitrago, L. / van Agthoven, J. / Zhang, Y. / Hara, R. / Tanaka, Y. / Okamoto, R. / Yasui, T. / Nakahata, T. / Imaeda, T. / Aso, ...Authors: Li, J. / Fukase, Y. / Shang, Y. / Zou, W. / Munoz-Felix, J. / Buitrago, L. / van Agthoven, J. / Zhang, Y. / Hara, R. / Tanaka, Y. / Okamoto, R. / Yasui, T. / Nakahata, T. / Imaeda, T. / Aso, K. / Zhou, Y. / Locuson, C. / Nesic, D. / Duggan, M. / Takagi, J. / Vaughan, R.D. / Walz, T. / Hodivala-Dilke, K. / Teitelbaum, S.L. / Arnaout, M.A. / Filizola, M. / Foley, M.A. / Coller, B.S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 647.8 KB | Display | ![]() |
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PDB format | ![]() | 533.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 60.3 KB | Display | |
Data in CIF | ![]() | 80.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ijeS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 105541.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 76042.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 4 types, 14 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 13 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/JUY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/JUY.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-MN / #8: Chemical | ChemComp-JUY / ( | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM Sodium Acetate pH 4.5, 800 mM Sodium Cholride, 12% PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 59916 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.145 / Rsym value: 0.052 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 3→3.11 Å / Num. unique obs: 5883 / CC1/2: 0.59 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IJE Resolution: 3.005→49.094 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 210.42 Å2 / Biso mean: 56.9907 Å2 / Biso min: 3.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.005→49.094 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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