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- PDB-6m9c: PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m9c | ||||||||||||
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Title | PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR Pseudotyrostatin | ||||||||||||
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![]() | Hydrolase/Hydrolase inhibitor / Serine-carboxyl proteinase / Hydrolase-hydrolase inhibitor complex | ||||||||||||
Function / homology | ![]() sedolisin / tripeptidyl-peptidase activity / periplasmic space / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Wlodawer, A. / Li, M. / Gustchina, A. / Dauter, Z. / Uchida, K. / Oyama, H. / Goldfarb, N.E. / Dunn, B.M. / Oda, K. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Dauter, Z. / Uchida, K. / Oyama, H. / Goldfarb, N.E. / Dunn, B.M. / Oda, K. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.3 KB | Display | ![]() |
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PDB format | ![]() | 112.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.4 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m8wC ![]() 6m8yC ![]() 6m9dC ![]() 6m9fC ![]() 1ga6S S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Details | As per the authors the biological assembly is a monomer |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 38108.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 101 / Gene: pcp / Production host: ![]() ![]() |
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#2: Protein/peptide | |
-Non-polymers , 4 types, 343 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #5: Chemical | ChemComp-ACY / #6: Water | ChemComp-HOH / | |
-Details
Compound details | THE UNBOUND INHIBITOR (CHAIN B) IS Pseudotyrostatin (IVA-TYR-TYB), WITH C-TERMINAL TYROSINAL. UPON ...THE UNBOUND INHIBITOR (CHAIN B) IS Pseudotyrostatin (IVA-TYR-TYB), WITH C-TERMINAL TYROSINAL. UPON REACTION THE INHIBITOR COVALENTLY |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Ammonium sulfate, guanidinium hydrochloride, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 41476 / % possible obs: 98 % / Observed criterion σ(F): 0.046 / Redundancy: 4.95 % / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.282 / Num. unique obs: 2099 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GA6 Resolution: 1.8→30 Å / Num. parameters: 12379 / Num. restraintsaints: 11394 / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: BABINET'S PRINCIPLE | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 2512 / Occupancy sum non hydrogen: 2721 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→30 Å
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Refine LS restraints |
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