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Yorodumi- PDB-5x0t: Crystal structure of CD147 C2 domain in complex with Fab of its m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x0t | |||||||||
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Title | Crystal structure of CD147 C2 domain in complex with Fab of its monoclonal antibody 6H8 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / CD147 / monoclonal antibody | |||||||||
Function / homology | Function and homology information Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / dendrite self-avoidance / response to mercury ion / cell-cell adhesion mediator activity / endothelial tube morphogenesis / neural retina development / Pyruvate metabolism ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / dendrite self-avoidance / response to mercury ion / cell-cell adhesion mediator activity / endothelial tube morphogenesis / neural retina development / Pyruvate metabolism / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / homophilic cell adhesion via plasma membrane adhesion molecules / D-mannose binding / decidualization / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / Integrin cell surface interactions / response to cAMP / embryo implantation / Degradation of the extracellular matrix / photoreceptor inner segment / positive regulation of endothelial cell migration / neutrophil chemotaxis / protein localization to plasma membrane / axon guidance / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / virus receptor activity / signaling receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / axon / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | |||||||||
Authors | Lin, P. / Zhang, M.-Y. / Ye, S. / Chen, X. / Yu, X.-L. / Zhang, R.-G. / Zhu, P. / Chen, Z.-N. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Crystal structure of CD147 C2 domain in complex with Fab of its monoclonal antibody Authors: Zhang, M.-Y. / Lin, P. / Zhu, P. / Chen, Z.-N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x0t.cif.gz | 204.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x0t.ent.gz | 169.7 KB | Display | PDB format |
PDBx/mmJSON format | 5x0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x0t_validation.pdf.gz | 475.1 KB | Display | wwPDB validaton report |
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Full document | 5x0t_full_validation.pdf.gz | 492.6 KB | Display | |
Data in XML | 5x0t_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 5x0t_validation.cif.gz | 53.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/5x0t ftp://data.pdbj.org/pub/pdb/validation_reports/x0/5x0t | HTTPS FTP |
-Related 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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-Components
#1: Antibody | Mass: 26331.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) #2: Antibody | Mass: 25913.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) #3: Protein | Mass: 9840.018 Da / Num. of mol.: 2 / Fragment: C2 domain, UNP residues 22-101 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BSG, UNQ6505/PRO21383 / Production host: Escherichia coli (E. coli) / References: UniProt: P35613 #4: 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: 2.05 Å3/Da / Density % sol: 40.11 % |
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Crystal grow | Temperature: 289 K / Method: evaporation Details: 0.2M lithium sulfate monohydrate, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→43.34 Å / Num. obs: 33828 / % possible obs: 97 % / Redundancy: 1 % / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.5→2.62 Å / Redundancy: 1 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 7.1 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Resolution: 2.5→37.161 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→37.161 Å
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Refine LS restraints |
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LS refinement shell |
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