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Yorodumi- PDB-3p92: Human mesotrypsin complexed with bovine pancreatic trypsin inhibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p92 | ||||||
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Title | Human mesotrypsin complexed with bovine pancreatic trypsin inhibitor variant (BPTI-K15R/R17G) | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / mesotrypsin / trypsin IV / canonical inhibitor / bovine pancreatic trypsin inibitor / BPTI / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / antimicrobial humoral response / Alpha-defensins / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin ...Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / antimicrobial humoral response / Alpha-defensins / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / zymogen activation / Antimicrobial peptides / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / endothelial cell migration / trypsin / serine protease inhibitor complex / digestion / serine-type peptidase activity / serine-type endopeptidase inhibitor activity / tertiary granule lumen / protease binding / serine-type endopeptidase activity / calcium ion binding / Neutrophil degranulation / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5992 Å | ||||||
Authors | Salameh, M.A. / Soares, A.S. / Radisky, E.S. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: The P2' residue is a key determinant of mesotrypsin specificity: engineering a high-affinity inhibitor with anticancer activity. Authors: Salameh, M.A. / Soares, A.S. / Hockla, A. / Radisky, D.C. / Radisky, E.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p92.cif.gz | 180 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p92.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 3p92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/3p92 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p92 | HTTPS FTP |
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-Related structure data
Related structure data | 3p95C 2r9pS S: Starting model for refinement C: citing same article (ref.) |
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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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 24257.457 Da / Num. of mol.: 1 / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N2U3, UniProt: P35030*PLUS, trypsin |
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#2: Protein | Mass: 6455.440 Da / Num. of mol.: 1 / Fragment: UNP Residues 36-93 / Mutation: K15R, R17G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P00974 |
#3: Chemical | ChemComp-CA / |
#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: 1.91 Å3/Da / Density % sol: 35.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG4000, 0.2M Na acetate and 100mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.599→33.851 Å / Num. all: 27380 / Num. obs: 27380 / % possible obs: 88.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 7.48 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 39.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R9P Resolution: 1.5992→33.851 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9196 / SU ML: 0.13 / σ(F): 0.18 / Phase error: 14.17 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.39 Å2 / ksol: 0.477 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.53 Å2 / Biso mean: 15.889 Å2 / Biso min: 3.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5992→33.851 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: 14
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