+Open data
-Basic information
Entry | Database: PDB / ID: 2g5n | ||||||
---|---|---|---|---|---|---|---|
Title | Indole-amidine Complexes with Bovine Trypsin | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / Trypsin amidine indole inhibition | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Kline, A.D. / Briggs, S.L. / Subramaniam, S. | ||||||
Citation | Journal: To be published Title: Ligand Epitoping By Proton NMR Chemical Shift Differences Authors: Kline, A.D. / Briggs, S.L. / Subramaniam, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2g5n.cif.gz | 57 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2g5n.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 2g5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g5n_validation.pdf.gz | 432.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2g5n_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 2g5n_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 2g5n_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/2g5n ftp://data.pdbj.org/pub/pdb/validation_reports/g5/2g5n | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Pancreas / References: UniProt: P00760, trypsin |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-23M / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Trypsin, final concentration of 0.6 mM, was dissolved in 20 mM HEPES pH 7.0, 10 mM calcium chloride, 3% DMSO, and 3 mM of ligand of interest (compounds 3, 6, and 9). The well solution ...Details: Trypsin, final concentration of 0.6 mM, was dissolved in 20 mM HEPES pH 7.0, 10 mM calcium chloride, 3% DMSO, and 3 mM of ligand of interest (compounds 3, 6, and 9). The well solution consisted of 100 mM Cacodylate pH 6.5, 200 mM ammonium sulfate, 50% PEG (17% to 28%). Drop ratio 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2005 / Details: Mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→43.12 Å / Num. all: 29622 / Num. obs: 29251 / % possible obs: 98.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 4 / Biso Wilson estimate: 17.2 Å2 |
Reflection shell | Resolution: 1.51→1.6 Å / % possible all: 97.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→43.12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2554828.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.202 Å2 / ksol: 0.392571 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→43.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.54 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|