+Open data
-Basic information
Entry | Database: PDB / ID: 8tfq | ||||||
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Title | Fab from C10-S66K antibody in complex with fentanyl | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / fentanyl / opioid. | ||||||
Function / homology | Chem-7V7 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pholcharee, T. / Wilson, I.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem Neurosci / Year: 2023 Title: An Engineered Human-Antibody Fragment with Fentanyl Pan-Specificity That Reverses Carfentanil-Induced Respiratory Depression. Authors: Eubanks, L.M. / Pholcharee, T. / Oyen, D. / Natori, Y. / Zhou, B. / Wilson, I.A. / Janda, K.D. #1: Journal: Biorxiv / Year: 2023 Title: An Engineered Human-Antibody Fragment with Fentanyl Pan-Specificity that Reverses Carfentanil-Induced Respiratory Depression. Authors: Eubanks, L.M. / Pholcharee, T. / Oyen, D. / Natori, Y. / Zhou, B. / Wilson, I.A. / Janda, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tfq.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tfq.ent.gz | 152.3 KB | Display | PDB format |
PDBx/mmJSON format | 8tfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/8tfq ftp://data.pdbj.org/pub/pdb/validation_reports/tf/8tfq | HTTPS FTP |
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-Related structure data
Related structure data | 8tfpC 8tfrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 22898.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 23831.975 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.66 Å3/Da / Density % sol: 53.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1.0 M Li-chloride, 10% PEG-6000, 0.1 M Bicine pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 87845 / % possible obs: 96.9 % / Redundancy: 3.2 % / CC1/2: 0.946 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 4175 / CC1/2: 0.776 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.72 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.67 / 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: 1.8→34.72 Å
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Refine LS restraints |
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LS refinement shell |
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