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Yorodumi- PDB-6fuh: Complement factor D in complex with the inhibitor (4-((3-(aminome... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fuh | ||||||
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Title | Complement factor D in complex with the inhibitor (4-((3-(aminomethyl)phenyl)amino)quinazolin-2-yl)-L-valine | ||||||
Components | Complement factor DFactor D | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / inhibitor / complex | ||||||
Function / homology | Function and homology information complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen ...complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.37 Å | ||||||
Authors | Mac Sweeney, A. / Ostermann, N. / Vulpetti, A. / Maibaum, J. / Erbel, P. / Lorthiois, E. / Yoon, T. / Randl, S. / Ruedisser, S. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2018 Title: Discovery and Design of First Benzylamine-Based Ligands Binding to an Unlocked Conformation of the Complement Factor D. Authors: Vulpetti, A. / Ostermann, N. / Randl, S. / Yoon, T. / Mac Sweeney, A. / Cumin, F. / Lorthiois, E. / Rudisser, S. / Erbel, P. / Maibaum, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fuh.cif.gz | 107.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fuh.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 6fuh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/6fuh ftp://data.pdbj.org/pub/pdb/validation_reports/fu/6fuh | HTTPS FTP |
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-Related structure data
Related structure data | 6ftyC 6ftzC 6fugC 6fuiC 6fujC 6futC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24739.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, PFD / Production host: Escherichia coli (E. coli) / References: UniProt: P00746, complement factor D |
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#2: Chemical | ChemComp-E88 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% PEG3350, 100 mM TRIS pH 8.5, 200 mM NH4SO2, 2 mM inhibitor |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→26.66 Å / Num. obs: 40221 / % possible obs: 93.7 % / Redundancy: 2.79 % / Net I/σ(I): 14.11 |
Reflection shell | Resolution: 1.37→1.42 Å |
-Processing
Software |
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Refinement | Resolution: 1.37→25.34 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.058 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.488 Å2
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Refinement step | Cycle: 1 / Resolution: 1.37→25.34 Å
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Refine LS restraints |
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