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Yorodumi- PDB-6fui: Complement factor D in complex with the inhibitor 3-((3-((3-(amin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fui | ||||||
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Title | Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol | ||||||
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: 1.38 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 | 6fui.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fui.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/6fui ftp://data.pdbj.org/pub/pdb/validation_reports/fu/6fui | HTTPS FTP |
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-Related structure data
Related structure data | 6ftyC 6ftzC 6fugC 6fuhC 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-E7W / ( |
#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: 2.12 Å3/Da / Density % sol: 41.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22-25% PEG3350, 100 mM HEPES pH 7.5 |
-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: Jun 10, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→30.12 Å / Num. obs: 41680 / % possible obs: 97.6 % / Redundancy: 2.8 % / Net I/σ(I): 15.54 |
Reflection shell | Resolution: 1.38→1.42 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.61 |
-Processing
Software |
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Refinement | Resolution: 1.38→29.14 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.525 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.064 / 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: 18.542 Å2
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Refinement step | Cycle: 1 / Resolution: 1.38→29.14 Å
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Refine LS restraints |
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