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Yorodumi- PDB-6fut: Complement factor D in complex with the inhibitor (S)-3'-(aminome... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fut | ||||||
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Title | Complement factor D in complex with the inhibitor (S)-3'-(aminomethyl)-N-(1,2,3,4-tetrahydronaphthalen-1-yl)-[1,1'-biphenyl]-3-carboxamide | ||||||
Components | Complement factor D | ||||||
Keywords | HYDROLASE / 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: 1.5 Å | ||||||
Authors | Mac Sweeney, A. / Vulpetti, A. / Erbel, P. / Lorthiois, E. / Maibaum, J. / Randl, 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 | 6fut.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fut.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fut_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6fut_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6fut_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 6fut_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/6fut ftp://data.pdbj.org/pub/pdb/validation_reports/fu/6fut | HTTPS FTP |
-Related structure data
Related structure data | 6ftyC 6ftzC 6fugC 6fuhC 6fuiC 6fujC 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-E82 / |
#3: Chemical | ChemComp-SIN / |
#4: 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: 3.06 Å3/Da / Density % sol: 59.74 % |
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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: Dec 12, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→57.1 Å / Num. obs: 52456 / % possible obs: 98 % / Redundancy: 5.68 % / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.46→1.51 Å / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Resolution: 1.5→57.05 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.946 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.061 / 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: 14.489 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→57.05 Å
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Refine LS restraints |
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