+Open data
-Basic information
Entry | Database: PDB / ID: 4jyt | ||||||
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Title | Crystal Structure of Matriptase in complex with Inhibitor | ||||||
Components | Suppressor of tumorigenicity 14 protein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / MATRIPTASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane ...matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / proteolysis / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Subramanya, H.S. / Ravi, B.C. / Ashok, K.N. / Chakshusmathi, G. / Ramesh, K.S. | ||||||
Citation | Journal: ACS MED.CHEM.LETT. / Year: 2013 Title: Discovery of Pyridyl Bis(oxy)dibenzimidamide Derivatives as Selective Matriptase Inhibitors Authors: Goswami, R. / Mukherjee, S. / Wohlfahrt, G. / Ghadiyaram, C. / Nagaraj, J. / Chandra, B.R. / Sistla, R.K. / Satyam, L.K. / Samiulla, D.S. / Moilanen, A. / Subramanya, H.S. / Ramachandra, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jyt.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jyt.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/4jyt ftp://data.pdbj.org/pub/pdb/validation_reports/jy/4jyt | HTTPS FTP |
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-Related structure data
Related structure data | 4jz1C 4jziC 1eaxS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26463.756 Da / Num. of mol.: 1 / Fragment: UNP residues 615-855 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ST14, PRSS14, SNC19, TADG15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Y6, matriptase |
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#2: Chemical | ChemComp-N4A / |
#3: 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: 2.26 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.1M Tris, 0.2M MgCl2, 20% PEG8000 , pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 33649 / Num. obs: 15425 / % possible obs: 92.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 2.6 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EAX Resolution: 2→25.91 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.442 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.188 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.854 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.91 Å
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Refine LS restraints |
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