+Open data
-Basic information
Entry | Database: PDB / ID: 4o9v | ||||||
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Title | Crystal structure of matriptase in complex with inhibitor | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / MATRIPTASE / Trypsin-like serine proteinase fold / Protease / Small molecule inhibitor / 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: 1.9 Å | ||||||
Authors | Rao, K.N. / Chandra, B.R. / Ashok, K.N. / Chakshusmathi, G. / Ramesh, K.S. / Subramanya, H.S. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2014 Title: Structure-guided discovery of 1,3,5 tri-substituted benzenes as potent and selective matriptase inhibitors exhibiting in vivo antitumor efficacy. Authors: Goswami, R. / Mukherjee, S. / Ghadiyaram, C. / Wohlfahrt, G. / Sistla, R.K. / Nagaraj, J. / Satyam, L.K. / Subbarao, K. / Palakurthy, R.K. / Gopinath, S. / Krishnamurthy, N.R. / Ikonen, T. / ...Authors: Goswami, R. / Mukherjee, S. / Ghadiyaram, C. / Wohlfahrt, G. / Sistla, R.K. / Nagaraj, J. / Satyam, L.K. / Subbarao, K. / Palakurthy, R.K. / Gopinath, S. / Krishnamurthy, N.R. / Ikonen, T. / Moilanen, A. / Subramanya, H.S. / Kallio, P. / Ramachandra, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o9v.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o9v.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 4o9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/4o9v ftp://data.pdbj.org/pub/pdb/validation_reports/o9/4o9v | HTTPS FTP |
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-Related structure data
Related structure data | 4o97C 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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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: Protein/peptide | Mass: 448.561 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 604-607 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 |
#3: Chemical | ChemComp-NT4 / |
#4: 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: 45.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.1M Tris pH 8.3 0.2M MgCl2, 20% PEG 8000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: 1.9→30 Å / Num. all: 37683 / Num. obs: 18653 / % possible obs: 94.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1843 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EAX Resolution: 1.9→28.03 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.898 / SU B: 3.207 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 14.538 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→28.03 Å
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Refine LS restraints |
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