+Open data
-Basic information
Entry | Database: PDB / ID: 1ezx | ||||||
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Title | CRYSTAL STRUCTURE OF A SERPIN:PROTEASE COMPLEX | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / protease-inhibitor complex / serpin / alpha-1-antitrypsin / trypsin / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / 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 / protease binding / collagen-containing extracellular matrix / endopeptidase activity / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / serine-type endopeptidase activity / 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) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Huntington, J.A. / Carrell, R.W. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Structure of a serpin-protease complex shows inhibition by deformation. Authors: Huntington, J.A. / Read, R.J. / Carrell, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ezx.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ezx.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ezx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/1ezx ftp://data.pdbj.org/pub/pdb/validation_reports/ez/1ezx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37692.922 Da / Num. of mol.: 1 Fragment: N-TERMINAL FRAGMENT OF PROTEOLYTIC CLEAVAGE AT MET358-SER359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Tissue fraction: PLASMA / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P01009 |
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#2: Protein/peptide | Mass: 4139.938 Da / Num. of mol.: 1 Fragment: C-TERMINAL FRAGMENT OF PROTEOLYTIC CLEAVAGE AT MET358-SER359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Tissue fraction: PLASMA / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P01009 |
#3: Protein | Mass: 25444.717 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin |
#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: 2.93 Å3/Da / Density % sol: 58.06 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3350, sodium citrate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.7 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 24803 / Num. obs: 24548 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 8 % / Rmerge(I) obs: 0.833 / Num. unique all: 3524 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 190117 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Resolution: 2.6→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target of Pannu and Read, 1996
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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