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- PDB-1bj1: VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bj1 | ||||||
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Title | VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY | ||||||
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![]() | IMMUNE SYSTEM / COMPLEX (ANTIBODY-ANTIGEN) / ANGIOGENIC FACTOR | ||||||
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 / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / 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 / negative regulation of epithelial to mesenchymal transition / platelet-derived growth factor receptor binding / surfactant homeostasis / 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 / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / 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 | ![]() ![]() ![]() | ||||||
![]() | Muller, Y.A. / Christinger, H.W. / De Vos, A.M. | ||||||
![]() | ![]() Title: VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface. Authors: Muller, Y.A. / Chen, Y. / Christinger, H.W. / Li, B. / Cunningham, B.C. / Lowman, H.B. / de Vos, A.M. #1: ![]() Title: Antibody Humanization Using Monovalent Phage Display Authors: Baca, M. / Presta, L.G. / O'Connor, S.J. / Wells, J.A. #2: ![]() Title: Humanization of an Anti-Vascular Endothelial Growth Factor Monoclonal Antibody for the Therapy of Solid Tumors and Other Disorders Authors: Presta, L.G. / Chen, H. / O'Connor, S.J. / Chisholm, V. / Meng, Y.G. / Krummen, L. / Winkler, M. / Ferrara, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.8 KB | Display | ![]() |
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PDB format | ![]() | 181.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484 KB | Display | ![]() |
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Full document | ![]() | 511.3 KB | Display | |
Data in XML | ![]() | 45.2 KB | Display | |
Data in CIF | ![]() | 65.5 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Components
#1: Antibody | Mass: 23471.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY Source: (gene. exp.) ![]() ![]() Description: HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY Production host: ![]() ![]() #2: Antibody | Mass: 24890.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY Source: (gene. exp.) ![]() ![]() Description: HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY Production host: ![]() ![]() #3: Protein | Mass: 11948.680 Da / Num. of mol.: 2 / Fragment: RECEPTOR BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE NUMBERING OF THE LIGHT CHAINS L AND J AS WELL AS OF THE HEAVY CHAINS H AND K IS SEQUENTIAL. ...THE NUMBERING OF THE LIGHT CHAINS L AND J AS WELL AS OF THE HEAVY CHAINS H AND K IS SEQUENTIAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 66 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting 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: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Mar 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.914 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 63147 / % possible obs: 96 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.4→2.48 Å / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 3.5 / % possible all: 81.3 |
Reflection shell | *PLUS % possible obs: 81.3 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VPF AND 1FVD Resolution: 2.4→8 Å / Rfactor Rfree error: 0.0035 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE MODEL IS UNUSUAL IN REGARD TO THE HIGH AVERAGE TEMPERATURE FACTOR OF 100 A2 OF THE CONSTANT DOMAIN OF THE SECOND FAB MOLECULE. HOWEVER THE USE OF NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS ...Details: THE MODEL IS UNUSUAL IN REGARD TO THE HIGH AVERAGE TEMPERATURE FACTOR OF 100 A2 OF THE CONSTANT DOMAIN OF THE SECOND FAB MOLECULE. HOWEVER THE USE OF NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS GREATLY RESTRICTS THE CONFORMATIONAL FREEDOM OF THIS PORTION TO THE WELL-DEFINED CONSTANT DOMAIN OF THE FIRST FAB FRAGMENT. MORE DETAILS CAN BE FOUND IN THE PRIMARY PUBLICATION.
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Displacement parameters | Biso mean: 42 Å2
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Refine analyze | Luzzati sigma a obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.4→2.48 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 54493 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.312 |