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- PDB-4k3j: Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta -
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Open data
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Basic information
Entry | Database: PDB / ID: 4k3j | ||||||
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Title | Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta | ||||||
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![]() | Transferase/Immune System/Growth Factor / ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of neuron projection regeneration / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / myoblast proliferation / regulation of p38MAPK cascade / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, X. / Starovasnik, M.A. | ||||||
![]() | ![]() Title: Monovalent antibody design and mechanism of action of onartuzumab, a MET antagonist with anti-tumor activity as a therapeutic agent. Authors: Merchant, M. / Ma, X. / Maun, H.R. / Zheng, Z. / Peng, J. / Romero, M. / Huang, A. / Yang, N.Y. / Nishimura, M. / Greve, J. / Santell, L. / Zhang, Y.W. / Su, Y. / Kaufman, D.W. / Billeci, K. ...Authors: Merchant, M. / Ma, X. / Maun, H.R. / Zheng, Z. / Peng, J. / Romero, M. / Huang, A. / Yang, N.Y. / Nishimura, M. / Greve, J. / Santell, L. / Zhang, Y.W. / Su, Y. / Kaufman, D.W. / Billeci, K.L. / Mai, E. / Moffat, B. / Lim, A. / Duenas, E.T. / Phillips, H.S. / Xiang, H. / Young, J.C. / Vande Woude, G.F. / Dennis, M.S. / Reilly, D.E. / Schwall, R.H. / Starovasnik, M.A. / Lazarus, R.A. / Yansura, D.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 467.8 KB | Display | ![]() |
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PDB format | ![]() | 386.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 337 KB | Display | ![]() |
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Full document | ![]() | 364.7 KB | Display | |
Data in XML | ![]() | 44.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1shyS 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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Unit cell |
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Components
-Hepatocyte growth ... , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 26038.086 Da / Num. of mol.: 1 / Fragment: unp residues 495-721 / Mutation: C604S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 60758.867 Da / Num. of mol.: 1 / Fragment: Sema and PSI domain, UNP residues 39-564 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08581, ![]() |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 24000.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: ![]() ![]() ![]() |
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#4: Antibody | Mass: 24363.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: ![]() ![]() ![]() |
-Sugars / Non-polymers , 2 types, 184 molecules 


#5: Sugar | ChemComp-NAG / ![]() |
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#6: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.85 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.1 M sodium cacodylate pH 6.2, 20% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→50 Å / Num. obs: 40382 / % possible obs: 98.9 % / Redundancy: 4 % / Rsym value: 0.074 / Net I/σ(I): 15.56 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.88 / Num. unique all: 3938 / Rsym value: 0.513 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1SHY Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / SU B: 29.924 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.704 / ESU R Free: 0.356 / 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: 52.103 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.874 Å / Total num. of bins used: 20
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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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