+Open data
-Basic information
Entry | Database: PDB / ID: 5ptp | |||||||||
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Title | STRUCTURE OF HYDROLASE (SERINE PROTEINASE) | |||||||||
Components | BETA TRYPSIN | |||||||||
Keywords | SERINE PROTEASE / HYDROLASE / DIGESTION / PANCREAS / ZYMOGEN | |||||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.34 Å | |||||||||
Authors | Stroud, R.M. / Finer-Moore, J. | |||||||||
Citation | Journal: Proteins / Year: 1992 Title: Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction. Authors: Finer-Moore, J.S. / Kossiakoff, A.A. / Hurley, J.H. / Earnest, T. / Stroud, R.M. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1979 Title: The Accuracy of Refined Protein Structures, Comparison of Two Independently Refined Models of Bovine Trypsin Authors: Chambers, J.L. / Stroud, R.M. #2: Journal: Acta Crystallogr.,Sect.B / Year: 1977 Title: Difference-Fourier Refinement of the Structure of Dip-Trypsin at 1.5 Angstroms Using a Minicomputer Technique Authors: Chambers, J.L. / Stroud, R.M. #3: Journal: PROTEASES AND BIOLOGICAL CONTROL / Year: 1975 Title: Structure-Function Relationships in the Serine Proteases Authors: Stroud, R.M. / Krieger, M. / Koeppe II, R.E. / Kossiakoff, A.A. / Chambers, J.L. #4: Journal: Biochem.Biophys.Res.Commun. / Year: 1974 Title: Silver Ion Inhibition of Serine Proteases: Crystallographic Study of Silver-Trypsin Authors: Chambers, J.L. / Christoph, G.G. / Krieger, M. / Kay, L. / Stroud, R.M. #5: Journal: J.Mol.Biol. / Year: 1974 Title: The Structure of Bovine Trypsin: Electron Density Maps of the Inhibited Enzyme at 5 a and at 2.7 A Resolution Authors: Stroud, R.M. / Kay, L.M. / Dickerson, R.E. #6: Journal: J.Mol.Biol. / Year: 1974 Title: Structure and Specific Binding of Trypsin: Comparison of Inhibited Derivatives and a Model for Substrate Binding Authors: Krieger, M. / Kay, L.M. / Stroud, R.M. #7: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972 Title: The Crystal and Molecular Structure of Dip-Inhibited Bovine Trypsin at 2.7 A Resolution Authors: Stroud, R.M. / Kay, L.M. / Dickerson, R.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ptp.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ptp.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ptp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ptp_validation.pdf.gz | 375.1 KB | Display | wwPDB validaton report |
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Full document | 5ptp_full_validation.pdf.gz | 380 KB | Display | |
Data in XML | 5ptp_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 5ptp_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/5ptp ftp://data.pdbj.org/pub/pdb/validation_reports/pt/5ptp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23446.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.34→7 Å Details: THE TRYPSIN IN THE CRYSTAL CONTAINS ABOUT 50 PER-CENT ALPHA-TRYPSIN WHICH IS AUTOLYTICALLY CLEAVED BETWEEN LYS 145 AND SER 146. THE DENSITY IN THE MAP AT THIS POINT IS WEAK BUT APPEARS TO ...Details: THE TRYPSIN IN THE CRYSTAL CONTAINS ABOUT 50 PER-CENT ALPHA-TRYPSIN WHICH IS AUTOLYTICALLY CLEAVED BETWEEN LYS 145 AND SER 146. THE DENSITY IN THE MAP AT THIS POINT IS WEAK BUT APPEARS TO ARISE FROM THE UNCLEAVED COMPONENT.
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Displacement parameters | Biso mean: 16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→7 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.152 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |