+Open data
-Basic information
Entry | Database: PDB / ID: 6ftz | ||||||
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Title | COMPLEMENT FACTOR D COMPLEXED WITH COMPOUND 6 | ||||||
Components | Complement factor D | ||||||
Keywords | HYDROLASE / SERINE PROTEASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Ostermann, N. | ||||||
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 | 6ftz.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ftz.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ftz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ftz_validation.pdf.gz | 678.8 KB | Display | wwPDB validaton report |
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Full document | 6ftz_full_validation.pdf.gz | 679.3 KB | Display | |
Data in XML | 6ftz_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 6ftz_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/6ftz ftp://data.pdbj.org/pub/pdb/validation_reports/ft/6ftz | HTTPS FTP |
-Related structure data
Related structure data | 6ftyC 6fugC 6fuhC 6fuiC 6fujC 6futC 5fbeS S: Starting model for refinement 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-E7E / ~{ |
#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: 2.11 Å3/Da / Density % sol: 41.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, 100 mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→49.98 Å / Num. obs: 23397 / % possible obs: 97.1 % / Redundancy: 3.09 % / Biso Wilson estimate: 11.64 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.62 |
Reflection shell | Resolution: 1.67→1.74 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.53 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FBE Resolution: 1.67→18.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.108
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Displacement parameters | Biso mean: 16.11 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→18.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.74 Å / Total num. of bins used: 12
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