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- PDB-1r64: The 2.2 A crystal structure of Kex2 protease in complex with Ac-A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r64 | |||||||||
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Title | The 2.2 A crystal structure of Kex2 protease in complex with Ac-Arg-Glu-Lys-boroArg peptidyl boronic acid inhibitor | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / KEX2 / KEXIN / PROTEASE / PROTEIN CONVERTASE / PROHORMONE PROCESSING / PROPROTEIN CONVERTASE / SUBTILISIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() kexin / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / peptide pheromone maturation / fungal-type vacuole / peptide hormone processing / trans-Golgi network / protein processing / serine-type endopeptidase activity / extracellular space / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Holyoak, T. / Kettner, C.A. / Petsko, G.A. / Fuller, R.S. / Ringe, D. | |||||||||
![]() | ![]() Title: Structural Basis for Differences in Substrate Selectivity in Kex2 and Furin Protein Convertases Authors: Holyoak, T. / Kettner, C.A. / Petsko, G.A. / Fuller, R.S. / Ringe, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.5 KB | Display | ![]() |
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PDB format | ![]() | 174.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 46.8 KB | Display | |
Data in CIF | ![]() | 67.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ot5S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 52640.016 Da / Num. of mol.: 2 / Fragment: Residues 121-601 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: KEX2 OR QDS1 OR YNL238W OR N1122 / Plasmid: PG5 / Production host: ![]() ![]() #2: Protein/peptide | |
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-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 4 types, 782 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-K / #7: Chemical | ChemComp-BTB / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.41 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Ammonium sulfate, DMSO, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2003 / Details: Bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 59902 / Num. obs: 59902 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.7 / % possible all: 69.5 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 69.5 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1OT5 Resolution: 2.2→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 207933.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.3647 Å2 / ksol: 0.381889 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å |