+Open data
-Basic information
Entry | Database: PDB / ID: 1yp9 | ||||||
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Title | Trypsin Inhibitor Complex | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / Trypsin / Inhibitor Complex / Barrel / 6 stranded beta-Sheet | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Fokkens, J. / Obst-Sander, U. / Heine, A. / Diederich, F. / Klebe, G. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2006 Title: A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates Authors: Fokkens, J. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yp9.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yp9.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yp9_validation.pdf.gz | 805.9 KB | Display | wwPDB validaton report |
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Full document | 1yp9_full_validation.pdf.gz | 808.9 KB | Display | |
Data in XML | 1yp9_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 1yp9_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/1yp9 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/1yp9 | HTTPS FTP |
-Related structure data
Related structure data | 1y3vC 1y3wC 1y3xC 1y3yC 1ypeC 1ypgC 1ypjC 1ypkC 1mtsS 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
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: blood / References: UniProt: P00760, trypsin | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-UIZ / ( | ||
#4: Chemical | #5: 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: 2.87 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, Imidazol, Calcium chloride, benzamidin hydrochlorid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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 / Date: Nov 21, 2004 / Details: Osmic morrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 13949 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.1 / Num. unique all: 15787 / Rsym value: 0.345 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1MTS Resolution: 2.1→10 Å / Num. parameters: 7311 / Num. restraintsaints: 6998 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 1578 / Occupancy sum non hydrogen: 1804.52 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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