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Yorodumi- PDB-2d26: Active site distortion is sufficient for proteinase inhibit secon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d26 | ||||||
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Title | Active site distortion is sufficient for proteinase inhibit second crystal structure of covalent serpin-proteinase complex | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERPINE PROTEINASE / SERPIN / COVALENT SERPIN-PROTEINASE COMP PROTEIN-PROTEIN INTERACTIONS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information pancreatic elastase / Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / acute-phase response / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...pancreatic elastase / Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / acute-phase response / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Dementiev, A. / Dobo, J. / Gettins, P.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Active Site Distortion Is Sufficient for Proteinase Inhibition by Serpins: Structure of the covalent complex of alpha 1-proteinase inhibitor with porcine pancreatic elastase Authors: Dementiev, A. / Dobo, J. / Gettins, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d26.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d26.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 2d26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/2d26 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/2d26 | HTTPS FTP |
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-Related 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: 40115.336 Da / Num. of mol.: 1 / Fragment: residues 1-358 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P01009 |
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#2: Protein/peptide | Mass: 4133.914 Da / Num. of mol.: 1 / Fragment: residues 359-394 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P01009 |
#3: Protein | Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase |
#4: 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: 2.1 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: PEG3350, pH 8.10, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2004 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.3→50 Å / Num. all: 9161 / Num. obs: 8959 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.5 | |||||||||
Reflection shell | Resolution: 3.3→3.45 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 5.7 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EZX, 1H9L Resolution: 3.3→50 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 235842.65 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.324779 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 63 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.45 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 7
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Xplor file |
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