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Yorodumi- PDB-4isl: Crystal Structure of the inactive Matriptase in complex with its ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4isl | ||||||
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Title | Crystal Structure of the inactive Matriptase in complex with its inhibitor HAI-1 | ||||||
Components |
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Keywords | hydrolase/hydrolase inhibitor / Beta barrel / Serine protease inhibitor / epithelium / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information epithelium development / Signaling by MST1 / matriptase / positive regulation of glial cell differentiation / epithelial cell morphogenesis involved in placental branching / acrosome reaction / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / Formation of the cornified envelope ...epithelium development / Signaling by MST1 / matriptase / positive regulation of glial cell differentiation / epithelial cell morphogenesis involved in placental branching / acrosome reaction / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / Formation of the cornified envelope / MET Receptor Activation / cellular response to BMP stimulus / epidermis development / keratinocyte differentiation / serine-type peptidase activity / extracellular matrix organization / neural tube closure / protein catabolic process / serine-type endopeptidase inhibitor activity / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Huang, M.D. / Zhao, B.Y. / Yuan, C. / Li, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal structures of matriptase in complex with its inhibitor hepatocyte growth factor activator inhibitor-1. Authors: Zhao, B. / Yuan, C. / Li, R. / Qu, D. / Huang, M. / Ngo, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4isl.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4isl.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 4isl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/4isl ftp://data.pdbj.org/pub/pdb/validation_reports/is/4isl | HTTPS FTP |
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-Related structure data
Related structure data | 4is5C 4isnC 4isoC 3p8gS 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
-Protein , 2 types, 2 molecules BA
#1: Protein | Mass: 6941.824 Da / Num. of mol.: 1 / Fragment: Kunitz domain I (unp residues 245-304) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HAI1, SPINT1, UNQ223/PRO256 / Plasmid: PMT/BIP/V5-his-A / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: O43278 |
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#2: Protein | Mass: 26461.783 Da / Num. of mol.: 1 / Fragment: Serine protease domain (unp residues 615-855) / Mutation: N164Q, S805A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS14, SNC19, ST14, TADG15 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q9Y5Y6, matriptase |
-Non-polymers , 5 types, 178 molecules
#3: Chemical | ChemComp-PG4 / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-GSH / | #7: 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: 2.57 Å3/Da / Density % sol: 52.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, 20% (w/v) polyethylene glycol 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.29→50 Å / Num. obs: 29858 / % possible obs: 98.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.057 / Χ2: 2.247 / Net I/σ(I): 21.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P8G Resolution: 2.29→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.534 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.75 Å2 / Biso mean: 21.6666 Å2 / Biso min: 10.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.35 Å / Total num. of bins used: 20
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