+Open data
-Basic information
Entry | Database: PDB / ID: 5nb7 | ||||||
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Title | Complement factor D | ||||||
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: 1.33 Å | ||||||
Authors | Mac Sweeney, A. / Ostermann, N. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo. Authors: Lorthiois, E. / Anderson, K. / Vulpetti, A. / Rogel, O. / Cumin, F. / Ostermann, N. / Steinbacher, S. / Mac Sweeney, A. / Delgado, O. / Liao, S.M. / Randl, S. / Rudisser, S. / Dussauge, S. / ...Authors: Lorthiois, E. / Anderson, K. / Vulpetti, A. / Rogel, O. / Cumin, F. / Ostermann, N. / Steinbacher, S. / Mac Sweeney, A. / Delgado, O. / Liao, S.M. / Randl, S. / Rudisser, S. / Dussauge, S. / Fettis, K. / Kieffer, L. / de Erkenez, A. / Yang, L. / Hartwieg, C. / Argikar, U.A. / La Bonte, L.R. / Newton, R. / Kansara, V. / Flohr, S. / Hommel, U. / Jaffee, B. / Maibaum, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nb7.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nb7.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/5nb7 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/5nb7 | HTTPS FTP |
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-Related structure data
Related structure data | 5narC 5natC 5nawC 5nb6C 5nbaC 1dsuS 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: 24596.965 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 | #3: Chemical | ChemComp-8NQ / | #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: 2.13 Å3/Da / Density % sol: 42.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 22% PEG 3350, 0.1 m HEPES pH 7.5, 50 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→30 Å / Num. obs: 47029 / % possible obs: 99 % / Redundancy: 3.3 % / Net I/σ(I): 18.51 |
Reflection shell | Resolution: 1.33→1.39 Å / Mean I/σ(I) obs: 3.6 / Num. unique obs: 5778 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DSU Resolution: 1.33→29.07 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.141 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.056 / 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: 18.658 Å2
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Refinement step | Cycle: 1 / Resolution: 1.33→29.07 Å
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Refine LS restraints |
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