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Open data
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Basic information
Entry | Database: PDB / ID: 5nb7 | ||||||
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Title | Complement factor D | ||||||
![]() | Complement factor D | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mac Sweeney, A. / Ostermann, N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.1 KB | Display | ![]() |
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PDB format | ![]() | 85.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.2 KB | Display | ![]() |
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Full document | ![]() | 804.2 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5narC ![]() 5natC ![]() 5nawC ![]() 5nb6C ![]() 5nbaC ![]() 1dsuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-8NQ / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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