+Open data
-Basic information
Entry | Database: PDB / ID: 5fbi | ||||||
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Title | COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND 3b | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Ostermann, N. / Zink, F. | ||||||
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 | 5fbi.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fbi.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/5fbi ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fbi | HTTPS FTP |
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-Related structure data
Related structure data | 5fahC 5fbeSC 5fckC 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-GOL / |
#3: Chemical | ChemComp-5WD / |
#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: 2.14 Å3/Da / Density % sol: 42.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1 Microliter of protein solution was mixed with 1 microliter of reservoir solution. Protein solution: 18.3 mg/ml factor D, 10 mM Tris pH 7.0, 100 mM sodium chloride; Reservoir solution: 22% ...Details: 1 Microliter of protein solution was mixed with 1 microliter of reservoir solution. Protein solution: 18.3 mg/ml factor D, 10 mM Tris pH 7.0, 100 mM sodium chloride; Reservoir solution: 22% PEG3350, 100 mM HEPES pH 7.5; Soaking and cryo: 0.5 ul 100 mM compound 3b in 90% DMSO was added to the crystal containing drop and incubated for 45 min followed by the addition of 0.5 ul glyerol and flash freezing in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9837 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 27, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9837 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→30.36 Å / Num. obs: 36222 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 19.34 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.5 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FBE Resolution: 1.47→30.36 Å / Cor.coef. Fo:Fc: 0.9611 / Cor.coef. Fo:Fc free: 0.9571 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.066
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Displacement parameters | Biso mean: 24.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.148 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→30.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.5 Å / Total num. of bins used: 18
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