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Yorodumi- PDB-5f03: TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f03 | ||||||
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Title | TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid | ||||||
Components | Tryptase beta-2 | ||||||
Keywords | HYDROLASE / HUMAN TRYPTASE / SERINE PROTEINASE | ||||||
Function / homology | Function and homology information tryptase / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / serine-type peptidase activity / defense response / collagen-containing extracellular matrix / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Banner, D. / Benz, J. / Joseph, C. / Kuglstatter, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: A Real-World Perspective on Molecular Design. Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / ...Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / Schulz-Gasch, T. / Woltering, T. / Stahl, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f03.cif.gz | 221.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f03.ent.gz | 176.5 KB | Display | PDB format |
PDBx/mmJSON format | 5f03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f03_validation.pdf.gz | 955.7 KB | Display | wwPDB validaton report |
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Full document | 5f03_full_validation.pdf.gz | 959 KB | Display | |
Data in XML | 5f03_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5f03_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f03 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f03 | HTTPS FTP |
-Related structure data
Related structure data | 5edbC 5edcC 5edeC 5edgC 5edhC 5ediC 5ezxC 5ezzC 5f00C 5f01C 5f02C 5i2rC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27491.426 Da / Num. of mol.: 2 / Mutation: NO Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: MAST CELLS / Gene: TPSB2, TPS2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P20231, UniProt: Q15661*PLUS, tryptase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 10000, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→67.88 Å / Num. obs: 43956 / % possible obs: 98.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.096 / Net I/av σ(I): 13.84 / Net I/σ(I): 0.0103 |
Reflection shell | Resolution: 1.94→2.06 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.78 / % possible all: 93.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in-house structure Resolution: 1.94→67.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.787 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.628 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→67.88 Å
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