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- PDB-6t9d: Crystal structure of a bispecific DutaFab in complex with human V... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t9d | ||||||
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Title | Crystal structure of a bispecific DutaFab in complex with human VEGF121 | ||||||
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![]() | IMMUNE SYSTEM / monoclonal antibody / bispecific antibody / Fab fragment / VEGF | ||||||
Function / homology | ![]() basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor binding / positive regulation of mast cell chemotaxis / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / bone trabecula formation / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lung vasculature development / lymphangiogenesis / eye photoreceptor cell development / endothelial cell chemotaxis / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of epithelial tube formation / 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 / vascular wound healing / positive regulation of protein localization to early endosome / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / camera-type eye morphogenesis / 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 / tube formation / positive regulation of vascular permeability / dopaminergic neuron differentiation / commissural neuron axon guidance / platelet-derived growth factor receptor binding / surfactant homeostasis / negative regulation of epithelial to mesenchymal transition / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / positive regulation of positive chemotaxis / endothelial cell proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of p38MAPK cascade / positive regulation of endothelial cell chemotaxis / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / branching involved in blood vessel morphogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / chemoattractant activity / outflow tract morphogenesis / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / vasculogenesis / positive regulation of osteoblast differentiation / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / homeostasis of number of cells within a tissue / positive regulation of protein autophosphorylation / positive regulation of endothelial cell proliferation / epithelial cell differentiation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kimbung, R. / Logan, D.T. / Beckmann, R. / Jensen, K. / Speck, J. / Fenn, S. / Kettenberger, H. | ||||||
![]() | ![]() Title: DutaFabs are engineered therapeutic Fab fragments that can bind two targets simultaneously. Authors: Beckmann, R. / Jensen, K. / Fenn, S. / Speck, J. / Krause, K. / Meier, A. / Roth, M. / Fauser, S. / Kimbung, R. / Logan, D.T. / Steegmaier, M. / Kettenberger, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6t9eC ![]() 1bj1S ![]() 1jpsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Components
#1: Antibody | Mass: 23502.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: VH region of DutaFab bispecific mAb / Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23820.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: VL region of DutaFab bispecific FAb / Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 14078.085 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.06 % / Description: Needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: VEGFA-121 from Peprotech, catalogue number 100-20A, was mixed at a 1:1 molar ratio to VEGF monomer. The complex was concentrated to 11 mg/ml. Crystallization involved hanging drop vapour ...Details: VEGFA-121 from Peprotech, catalogue number 100-20A, was mixed at a 1:1 molar ratio to VEGF monomer. The complex was concentrated to 11 mg/ml. Crystallization involved hanging drop vapour diffusion against 0.1 M MES pH 6.5 and 1.6 M magnesium sulphate. Crystals grew in about 120 days and were frozen in liquid nitrogen with 20 % glycerol as cryoprotectant. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2014 / Details: KB MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 28318 / % possible obs: 98.9 % / Redundancy: 3 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.212 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.9→3.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4494 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BJ1, 1JPS Resolution: 2.905→29.294 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.808 / SU B: 24.612 / SU ML: 0.432 / Cross valid method: FREE R-VALUE / ESU R Free: 0.461 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.023 Å2
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Refinement step | Cycle: LAST / Resolution: 2.905→29.294 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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