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Yorodumi- PDB-1hp7: A 2.1 ANGSTROM STRUCTURE OF AN UNCLEAVED ALPHA-1-ANTITRYPSIN SHOW... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hp7 | ||||||
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Title | A 2.1 ANGSTROM STRUCTURE OF AN UNCLEAVED ALPHA-1-ANTITRYPSIN SHOWS VARIABILITY OF THE REACTIVE CENTER AND OTHER LOOPS | ||||||
Components | ALPHA-1-ANTITRYPSIN | ||||||
Keywords | PROTEIN BINDING / uncleaved alpha-1-antitrypsin serpin | ||||||
Function / homology | Function and homology information 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 / acute-phase response / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / serine-type endopeptidase inhibitor activity / blood coagulation ...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 / acute-phase response / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / serine-type endopeptidase inhibitor activity / blood coagulation / Platelet degranulation / protease binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.1 Å | ||||||
Authors | Kim, S.-J. / Woo, J.-R. / Seo, E.J. / Yu, M.-H. / Ryu, S.-E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: A 2.1 A resolution structure of an uncleaved alpha(1)-antitrypsin shows variability of the reactive center and other loops. Authors: Kim, S. / Woo, J. / Seo, E.J. / Yu, M. / Ryu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hp7.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hp7.ent.gz | 67.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hp7_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 1hp7_full_validation.pdf.gz | 449.7 KB | Display | |
Data in XML | 1hp7_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1hp7_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/1hp7 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/1hp7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 44331.258 Da / Num. of mol.: 1 / Mutation: A70G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PEAT8 / Production host: Escherichia coli (E. coli) / References: UniProt: P01009 | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BME / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 25 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 23044 / % possible obs: 91 % / Redundancy: 3.2 % / Num. measured all: 74819 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 85 % / Rmerge(I) obs: 0.354 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→99 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→99 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 99 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.219 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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