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- PDB-7npl: ALPHA-1 ANTITRYPSIN (C232S) COMPLEXED WITH cmpd 11 -

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Basic information

Entry
Database: PDB / ID: 7npl
TitleALPHA-1 ANTITRYPSIN (C232S) COMPLEXED WITH cmpd 11
ComponentsAlpha-1-antitrypsin
KeywordsUNKNOWN FUNCTION / apha1 antitrypsin (C232S) / SERPIN / INHIBITOR / COMPLEX
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
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
Similarity search - Domain/homology
Chem-UKZ / Alpha-1-antitrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsChung, C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: The development of highly potent and selective small molecule correctors of Z alpha 1 -antitrypsin misfolding.
Authors: Liddle, J. / Pearce, A.C. / Arico-Muendel, C. / Belyanskaya, S. / Brewster, A. / Brown, M. / Chung, C.W. / Denis, A. / Dodic, N. / Dossang, A. / Eddershaw, P. / Klimaszewska, D. / Haq, I. / ...Authors: Liddle, J. / Pearce, A.C. / Arico-Muendel, C. / Belyanskaya, S. / Brewster, A. / Brown, M. / Chung, C.W. / Denis, A. / Dodic, N. / Dossang, A. / Eddershaw, P. / Klimaszewska, D. / Haq, I. / Holmes, D.S. / Jagger, A. / Jakhria, T. / Jigorel, E. / Lind, K. / Messer, J. / Neu, M. / Olszewski, A. / Ronzoni, R. / Rowedder, J. / Rudiger, M. / Skinner, S. / Smith, K.J. / Trottet, L. / Uings, I. / Zhu, Z. / Irving, J.A. / Lomas, D.A.
History
DepositionFeb 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-1-antitrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0753
Polymers45,5961
Non-polymers4792
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.12, 39.2, 90.45
Angle α, β, γ (deg.)90, 105.38, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-1-antitrypsin / Alpha-1 protease inhibitor / Alpha-1-antiproteinase / Serpin A1


Mass: 45595.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Production host: Escherichia coli (E. coli) / References: UniProt: P01009
#2: Chemical ChemComp-UKZ / N-((1S,2R)-1-(3-chloro-2-methylphenyl)-1-hydroxypentan-2-yl)-2-oxoindoline-4-carboxamide / ~{N}-[(1~{S},2~{R})-1-(3-chloranyl-2-methyl-phenyl)-1-oxidanyl-pentan-2-yl]-2-oxidanylidene-1,3-dihydroindole-4-carboxamide / N-[(1S,2R)-1-(3-chloranyl-2-methyl-phenyl)-1-oxidanyl-pentan-2-yl]-2-oxidanylidene-1,3-dihydroindole-4-carboxamide


Mass: 386.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 14% PEG1500 0.1M MES pH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.82→55 Å / Num. obs: 26992 / % possible obs: 77.2 % / Redundancy: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.033 / Net I/σ(I): 15.4
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.714 / Num. unique obs: 642 / CC1/2: 0.471 / % possible all: 24.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house

Resolution: 1.82→55.02 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.143
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1357 -RANDOM
Rwork0.1924 ---
obs0.1937 26990 77 %-
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.2946 Å20 Å2-7.0252 Å2
2---7.1045 Å20 Å2
3---0.8098 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.82→55.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 33 79 2959
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082939HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.983970HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1035SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes490HARMONIC5
X-RAY DIFFRACTIONt_it2939HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion382SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2223SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion17.48
LS refinement shellResolution: 1.82→1.86 Å
RfactorNum. reflection% reflection
Rfree0.3199 32 -
Rwork0.2657 --
obs0.269 540 24.81 %
Refinement TLS params.Origin x: -26.8758 Å / Origin y: -0.7872 Å / Origin z: 21.0478 Å
111213212223313233
T-0.0095 Å2-0.0892 Å2-0.0331 Å2--0.0178 Å2-0.0014 Å2---0.0633 Å2
L3.6904 °20.8592 °2-1.6723 °2-0.7333 °2-0.5981 °2--1.5715 °2
S-0.1545 Å °-0.1519 Å °0.0876 Å °-0.1519 Å °0.2337 Å °-0.1867 Å °0.0876 Å °-0.1867 Å °-0.0792 Å °
Refinement TLS groupSelection details: { A|* }

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