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Yorodumi- PDB-6qmt: Complement factor D in complex with the inhibitor 2-(2-(3'-(amino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qmt | ||||||
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Title | Complement factor D in complex with the inhibitor 2-(2-(3'-(aminomethyl)-[1,1'-biphenyl]-3-carboxamido)phenyl)acetic acid | ||||||
Components | Complement factor D | ||||||
Keywords | HYDROLASE / Complement factor D / inhibitor | ||||||
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: 1.8 Å | ||||||
Authors | Karki, R. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D. / Liu, D. / Jendza, K. / Gelin, C.F. / Solovay, C. / Mac Sweeeny, A. ...Karki, R. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D. / Liu, D. / Jendza, K. / Gelin, C.F. / Solovay, C. / Mac Sweeeny, A. / Delgado, O. / Crowley, M. / Liao, S.-M. / Argikar, U.A. / Flohr, S. / La Bonte, L.R. / Lorthiois, E.L. / Vulpetti, A. / Cumin, F. / Brown, A. / Adams, C. / Jaffee, B. / Mogi, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Design, Synthesis, and Preclinical Characterization of Selective Factor D Inhibitors Targeting the Alternative Complement Pathway. Authors: Karki, R.G. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D.B. / Liu, D. / Ji, N. / Jendza, K. / Gelin, C.F. / Mac Sweeney, A. / Solovay, C. / Delgado, O. / Crowley, M. / Liao, S.M. ...Authors: Karki, R.G. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D.B. / Liu, D. / Ji, N. / Jendza, K. / Gelin, C.F. / Mac Sweeney, A. / Solovay, C. / Delgado, O. / Crowley, M. / Liao, S.M. / Argikar, U.A. / Flohr, S. / La Bonte, L.R. / Lorthiois, E.L. / Vulpetti, A. / Brown, A. / Long, D. / Prentiss, M. / Gradoux, N. / de Erkenez, A. / Cumin, F. / Adams, C. / Jaffee, B. / Mogi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qmt.cif.gz | 103.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qmt.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qmt_validation.pdf.gz | 942.9 KB | Display | wwPDB validaton report |
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Full document | 6qmt_full_validation.pdf.gz | 948.9 KB | Display | |
Data in XML | 6qmt_validation.xml.gz | 19 KB | Display | |
Data in CIF | 6qmt_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/6qmt ftp://data.pdbj.org/pub/pdb/validation_reports/qm/6qmt | HTTPS FTP |
-Related structure data
Related structure data | 6qmrC 1dsuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27097.936 Da / Num. of mol.: 2 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 28.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEGME 3350, 100 mM Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→61.41 Å / Num. obs: 37403 / % possible obs: 92.9 % / Observed criterion σ(F): -3 / Redundancy: 2.35 % / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.063 / Net I/σ(I): 10.93 |
Reflection shell | Resolution: 1.63→1.73 Å / Redundancy: 2.15 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 5507 / Rrim(I) all: 0.4 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DSU Resolution: 1.8→35.6 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.158 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.8 Å2 / Biso mean: 25.871 Å2 / Biso min: 3 Å2
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Refinement step | Cycle: final / Resolution: 1.8→35.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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