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Open data
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Basic information
Entry | Database: PDB / ID: 3ndd | ||||||
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Title | Cleaved antitrypsin with P10 Pro, and P9-P6 Asp | ||||||
![]() | (Alpha-1-antitrypsin) x 2 | ||||||
![]() | HYDROLASE INHIBITOR / serpin | ||||||
Function / homology | ![]() 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 / 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 ...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 / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamasaki, M. / Sendall, T.J. / Huntington, J.A. | ||||||
![]() | ![]() Title: Loop-sheet mechanism of serpin polymerization tested by reactive center loop mutations Authors: Yamasaki, M. / Sendall, T.J. / Harris, L.E. / Lewis, G.M.W. / Huntington, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.3 KB | Display | ![]() |
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PDB format | ![]() | 132.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ndfC ![]() 1ezxS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 38628.676 Da / Num. of mol.: 1 Fragment: P1 cleaved antitrypsin, nterm, UNP residues 46-382 Mutation: C232A, G349P, A350D, M351D, F352D, L353D, M358R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 4139.938 Da / Num. of mol.: 1 Fragment: P1 cleaved antitrypsin, cterm, UNP residues 383-418 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6 Details: 0.1M MES/NaOH, 30% PEG 400, 35% glycerol, pH 6, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→34.04 Å / Num. all: 55516 / Num. obs: 55516 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8057 / Rsym value: 0.496 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EZX Resolution: 1.5→32.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.032 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.412 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→32.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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