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- PDB-1kct: ALPHA1-ANTITRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1kct
TitleALPHA1-ANTITRYPSIN
ComponentsALPHA1-ANTITRYPSIN
KeywordsSERINE PROTEASE INHIBITOR / SERPIN / GLYCOPROTEIN
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 / 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 / collagen-containing extracellular matrix / protease binding / 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
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.46 Å
AuthorsSong, H.K. / Suh, S.W.
CitationJournal: FEBS Lett. / Year: 1995
Title: Crystal structure of an uncleaved alpha 1-antitrypsin reveals the conformation of its inhibitory reactive loop.
Authors: Song, H.K. / Lee, K.N. / Kwon, K.S. / Yu, M.H. / Suh, S.W.
History
DepositionAug 6, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA1-ANTITRYPSIN


Theoretical massNumber of molelcules
Total (without water)44,3041
Polymers44,3041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.870, 39.980, 92.420
Angle α, β, γ (deg.)90.00, 102.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ALPHA1-ANTITRYPSIN / ALPHA1-PROTEINASE INHIBITOR


Mass: 44304.281 Da / Num. of mol.: 1 / Mutation: T59A, T68A, A70G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: A1AT / Plasmid: PET-8C / Species (production host): Escherichia coli / Gene (production host): A1AT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01009

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 48 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlinhibitor1drop
250 mMTris-HCl1drop
328.5 %(w/v)PEG40001reservoir
4100 mMTris-HCl1reservoir
5200 mMlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Nov 10, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 4380 / % possible obs: 82.6 % / Observed criterion σ(I): 0.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.106
Reflection shellResolution: 3.46→3.6 Å / % possible all: 63

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementResolution: 3.46→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.184 --
obs0.184 4079 81.2 %
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.46→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 0 0 2965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.42
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.94
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.42
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.94

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