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Yorodumi- PDB-7u64: Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u64 | ||||||
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Title | Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl | ||||||
Components | (HY6-F9.6 Fab ...) x 2 | ||||||
Keywords | IMMUNE SYSTEM / mAb / opioid | ||||||
Function / homology | Chem-7V7 / ACETATE ION Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Rodarte, J.V. / Pancera, M.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2023 Title: Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding. Authors: Rodarte, J.V. / Baehr, C. / Hicks, D. / Liban, T.L. / Weidle, C. / Rupert, P.B. / Jahan, R. / Wall, A. / McGuire, A.T. / Strong, R.K. / Runyon, S. / Pravetoni, M. / Pancera, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u64.cif.gz | 1019.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u64.ent.gz | 674.2 KB | Display | PDB format |
PDBx/mmJSON format | 7u64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u64_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 7u64_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 7u64_validation.xml.gz | 165.1 KB | Display | |
Data in CIF | 7u64_validation.cif.gz | 235.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/7u64 ftp://data.pdbj.org/pub/pdb/validation_reports/u6/7u64 | HTTPS FTP |
-Related structure data
Related structure data | 7u61C 7u62C 7u63C 4lexS S: Starting model for refinement 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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Unit cell |
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-Components
-Antibody , 2 types, 18 molecules ACEGIKMOQBDFHJLNPR
#1: Antibody | Mass: 24345.039 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #2: Antibody | Mass: 24000.818 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
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-Non-polymers , 4 types, 2911 molecules
#3: Chemical | ChemComp-7V7 / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Details
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: 2.86 Å3/Da / Density % sol: 56.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.8M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97388 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97388 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.75→43.33 Å / Num. obs: 475987 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 16.94 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.068 / Rrim(I) all: 0.155 / Net I/σ(I): 7.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LEX Resolution: 1.75→43.33 Å / SU ML: 0.1994 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.933 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→43.33 Å
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Refine LS restraints |
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LS refinement shell |
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