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Yorodumi- PDB-6rav: Complement factor B protease domain in complex with the reversibl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rav | |||||||||
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Title | Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid | |||||||||
Components | Complement factor B | |||||||||
Keywords | HYDROLASE / Complement / immune / inhibitor / c3 convertase | |||||||||
Function / homology | Function and homology information alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle ...alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Adams, C.M. / Sellner, H. / Ehara, T. / Mac Sweeney, A. / Crowley, M. / Anderson, K. / Karki, R. / Mainolfi, N. / Valeur, E. / Sirockin, F. ...Adams, C.M. / Sellner, H. / Ehara, T. / Mac Sweeney, A. / Crowley, M. / Anderson, K. / Karki, R. / Mainolfi, N. / Valeur, E. / Sirockin, F. / Gerhartz, B. / Erbel, P. / Hughes, N. / Smith, T.M. / Cumin, F. / Argikar, U. / Mogi, M. / Sedrani, R. / Wiesmann, C. / Jaffee, B. / Maibaum, J. / Flohr, S. / Harrison, R. / Eder, J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Small-molecule factor B inhibitor for the treatment of complement-mediated diseases. Authors: Schubart, A. / Anderson, K. / Mainolfi, N. / Sellner, H. / Ehara, T. / Adams, C.M. / Mac Sweeney, A. / Liao, S.M. / Crowley, M. / Littlewood-Evans, A. / Sarret, S. / Wieczorek, G. / Perrot, ...Authors: Schubart, A. / Anderson, K. / Mainolfi, N. / Sellner, H. / Ehara, T. / Adams, C.M. / Mac Sweeney, A. / Liao, S.M. / Crowley, M. / Littlewood-Evans, A. / Sarret, S. / Wieczorek, G. / Perrot, L. / Dubost, V. / Flandre, T. / Zhang, Y. / Smith, R.J.H. / Risitano, A.M. / Karki, R.G. / Zhang, C. / Valeur, E. / Sirockin, F. / Gerhartz, B. / Erbel, P. / Hughes, N. / Smith, T.M. / Cumin, F. / Argikar, U.A. / Haraldsson, B. / Mogi, M. / Sedrani, R. / Wiesmann, C. / Jaffee, B. / Maibaum, J. / Flohr, S. / Harrison, R. / Eder, J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Small-molecule factor B inhibitor for the treatment of complement-mediated diseases. Authors: Schubart, A. / Anderson, K. / Mainolfi, N. / Sellner, H. / Ehara, T. / Adams, C.M. / Mac Sweeney, A. / Liao, S.M. / Crowley, M. / Littlewood-Evans, A. / Sarret, S. / Wieczorek, G. / Perrot, ...Authors: Schubart, A. / Anderson, K. / Mainolfi, N. / Sellner, H. / Ehara, T. / Adams, C.M. / Mac Sweeney, A. / Liao, S.M. / Crowley, M. / Littlewood-Evans, A. / Sarret, S. / Wieczorek, G. / Perrot, L. / Dubost, V. / Flandre, T. / Zhang, Y. / Smith, R.J.H. / Risitano, A.M. / Karki, R.G. / Zhang, C. / Valeur, E. / Sirockin, F. / Gerhartz, B. / Erbel, P. / Hughes, N. / Smith, T.M. / Cumin, F. / Argikar, U.A. / Haraldsson, B. / Mogi, M. / Sedrani, R. / Wiesmann, C. / Jaffee, B. / Maibaum, J. / Flohr, S. / Harrison, R. / Eder, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rav.cif.gz | 239.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rav.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6rav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rav_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6rav_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6rav_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 6rav_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/6rav ftp://data.pdbj.org/pub/pdb/validation_reports/ra/6rav | HTTPS FTP |
-Related structure data
Related structure data | 6qswC 6qsxC 1dleS 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: 32955.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFB, BF, BFD / Production host: Drosophila melanogaster (fruit fly) References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: 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: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 24 % (w/v) PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 2mM inhibitor |
-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: Jun 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.723 Å / Num. obs: 68802 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.081 / Net I/σ(I): 10.82 |
Reflection shell | Resolution: 1.7→1.77 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7743 / Rrim(I) all: 0.991 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1dle Resolution: 1.7→48.723 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.89 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.108 Details: Hydrogens have been added in their 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.753 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→48.723 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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