+Open data
-Basic information
Entry | Database: PDB / ID: 5fck | ||||||
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Title | COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND 5 | ||||||
Components | Complement factor DFactor D | ||||||
Keywords | HYDROLASE | ||||||
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: 1.86 Å | ||||||
Authors | Mac Sweeney, A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Small-molecule factor D inhibitors targeting the alternative complement pathway. Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. ...Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. / Dussauge, S. / Hughes, N. / Delgado, O. / Hommel, U. / Gould, T. / Mac Sweeney, A. / Gerhartz, B. / Cumin, F. / Flohr, S. / Schubart, A. / Jaffee, B. / Harrison, R. / Risitano, A.M. / Eder, J. / Anderson, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fck.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fck.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/5fck ftp://data.pdbj.org/pub/pdb/validation_reports/fc/5fck | HTTPS FTP |
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-Related structure data
Related structure data | 5fahC 5fbeSC 5fbiC 5fcrC 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-5WC / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1 uL FD solution (18 mg/mL FD, 10 mM Tris pH 7.0, 100 mM NaCl) was mixed with 1 uL reservoir solution (25% PEG3350, 100 mM TRIS pH 8.0) and equilibrated against 1 mL reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→22.87 Å / Num. obs: 14490 / % possible obs: 89.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.86→1.91 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.194 / % possible all: 49.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FBE Resolution: 1.86→22.87 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.761 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.035 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→22.87 Å
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Refine LS restraints |
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