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Yorodumi- PDB-3rxd: Crystal structure of Trypsin complexed with (3-methoxyphenyl)meth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rxd | ||||||
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Title | Crystal structure of Trypsin complexed with (3-methoxyphenyl)methanamine | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Trypsin-like serine proteases / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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: 1.7 Å | ||||||
Authors | Yamane, J. / Yao, M. / Zhou, Y. / Tanaka, I. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2011 Title: In-crystal affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities Authors: Yamane, J. / Yao, M. / Zhou, Y. / Hiramatsu, Y. / Fujiwara, K. / Yamaguchi, T. / Yamaguchi, H. / Togame, H. / Tsujishita, H. / Takemoto, H. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rxd.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rxd.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 3rxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/3rxd ftp://data.pdbj.org/pub/pdb/validation_reports/rx/3rxd | HTTPS FTP |
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-Related structure data
Related structure data | 3atiC 3atkC 3atlC 3atmC 3rxaC 3rxbC 3rxcC 3rxeC 3rxfC 3rxgC 3rxhC 3rxiC 3rxjC 3rxkC 3rxlC 3rxmC 3rxoC 3rxpC 3rxqC 3rxrC 3rxsC 3rxtC 3rxuC 3rxvC 1s0rS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 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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-Non-polymers , 5 types, 316 molecules
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SZ4 / | #6: 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: 45.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl, 30% PEG 3350, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 23997 / Num. obs: 23517 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S0R Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.682 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R Free: 0.099 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.044 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0.099 / Total num. of bins used: 20
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