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- PDB-7ael: alpha 1-antitrypsin (C232S) complexed with GSK716 -

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Basic information

Entry
Database: PDB / ID: 7ael
Titlealpha 1-antitrypsin (C232S) complexed with GSK716
ComponentsAlpha-1-antitrypsin
KeywordsPROTEIN BINDING / SERPIN / SERINE PROTEASE INHIBITOR
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-R7Z / Alpha-1-antitrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsChung, C.
CitationJournal: Embo Mol Med / Year: 2021
Title: Development of a small molecule that corrects misfolding and increases secretion of Z alpha 1 -antitrypsin.
Authors: Lomas, D.A. / Irving, J.A. / Arico-Muendel, C. / Belyanskaya, S. / Brewster, A. / Brown, M. / Chung, C.W. / Dave, H. / Denis, A. / Dodic, N. / Dossang, A. / Eddershaw, P. / Klimaszewska, D. ...Authors: Lomas, D.A. / Irving, J.A. / Arico-Muendel, C. / Belyanskaya, S. / Brewster, A. / Brown, M. / Chung, C.W. / Dave, H. / Denis, A. / Dodic, N. / Dossang, A. / Eddershaw, P. / Klimaszewska, D. / Haq, I. / Holmes, D.S. / Hutchinson, J.P. / Jagger, A.M. / Jakhria, T. / Jigorel, E. / Liddle, J. / Lind, K. / Marciniak, S.J. / Messer, J. / Neu, M. / Olszewski, A. / Ordonez, A. / Ronzoni, R. / Rowedder, J. / Rudiger, M. / Skinner, S. / Smith, K.J. / Terry, R. / Trottet, L. / Uings, I. / Wilson, S. / Zhu, Z. / Pearce, A.C.
History
DepositionSep 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Alpha-1-antitrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0623
Polymers45,5961
Non-polymers4662
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-19 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.954, 39.592, 90.517
Angle α, β, γ (deg.)90.000, 104.961, 90.000
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
Details: TFNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLN FNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSE AFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFEVK ...Details: TFNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLN FNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSE AFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFEVK DTEEEDFHVDQVTTVKVPMMKRLGMFNIQHSKKLSSWVLLMKYLGNATAIFFLPDEGKLQ HLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNGADLSGV TEEAPLKLSKAVHKAVLTIDPMSIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQ
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Production host: Escherichia coli (E. coli) / References: UniProt: P01009
#2: Chemical ChemComp-R7Z / ~{N}-[(1~{S},2~{R})-1-(3-fluoranyl-2-methyl-phenyl)-1-oxidanyl-pentan-2-yl]-2-oxidanylidene-1,3-dihydroindole-4-carboxamide


Mass: 370.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23FN2O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 22% PEG1500, 0.2M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.76→55.05 Å / Num. obs: 38875 / % possible obs: 99.2 % / Redundancy: 3.3 % / CC1/2: 0.999 / Net I/σ(I): 19.61
Reflection shellResolution: 1.76→1.823 Å / Rmerge(I) obs: 0.5007 / Num. unique obs: 3853 / CC1/2: 0.805

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal

Resolution: 1.76→55.05 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.835 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.123 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2239 1916 4.929 %
Rwork0.1893 36959 -
all0.191 --
obs-38875 98.914 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 41.746 Å2
Baniso -1Baniso -2Baniso -3
1--0.974 Å20 Å20.712 Å2
2--1.199 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.76→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 32 289 3158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132964
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172774
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.6384014
X-RAY DIFFRACTIONr_angle_other_deg1.2341.5846476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.425.036137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57415537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.296156
X-RAY DIFFRACTIONr_chiral_restr0.0560.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_nbd_refined0.1930.2481
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.22441
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21395
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2156
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.28
X-RAY DIFFRACTIONr_nbd_other0.2050.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.26
X-RAY DIFFRACTIONr_mcbond_it2.9445.4731446
X-RAY DIFFRACTIONr_mcbond_other2.9455.4691445
X-RAY DIFFRACTIONr_mcangle_it4.03312.281811
X-RAY DIFFRACTIONr_mcangle_other4.03212.2871812
X-RAY DIFFRACTIONr_scbond_it4.1136.1631518
X-RAY DIFFRACTIONr_scbond_other4.1156.1641515
X-RAY DIFFRACTIONr_scangle_it6.55513.4382203
X-RAY DIFFRACTIONr_scangle_other6.5613.4412198
X-RAY DIFFRACTIONr_lrange_it7.96249.7323141
X-RAY DIFFRACTIONr_lrange_other7.96149.7233142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.8040.321310.282727X-RAY DIFFRACTION98.6878
1.804-1.8540.2561380.252620X-RAY DIFFRACTION98.924
1.854-1.9070.2591380.2332590X-RAY DIFFRACTION99.1639
1.907-1.9660.2561290.2242503X-RAY DIFFRACTION99.0964
1.966-2.030.2181130.2052403X-RAY DIFFRACTION99.1332
2.03-2.1020.2511310.2142377X-RAY DIFFRACTION99.2089
2.102-2.1810.2351310.212224X-RAY DIFFRACTION98.9912
2.181-2.270.214950.1952204X-RAY DIFFRACTION99.0948
2.27-2.3710.2161070.1932089X-RAY DIFFRACTION99.3216
2.371-2.4860.2671070.1882023X-RAY DIFFRACTION99.1159
2.486-2.6210.2411070.1891902X-RAY DIFFRACTION99.112
2.621-2.7790.2960.1831792X-RAY DIFFRACTION99.4208
2.779-2.9710.234810.1911701X-RAY DIFFRACTION98.7258
2.971-3.2090.263730.2021602X-RAY DIFFRACTION98.9953
3.209-3.5150.226790.2041456X-RAY DIFFRACTION98.3344
3.515-3.9290.248810.1831317X-RAY DIFFRACTION98.0365
3.929-4.5350.178720.1551167X-RAY DIFFRACTION98.4897
4.535-5.5510.177500.1521009X-RAY DIFFRACTION99.1573
5.551-7.8340.201310.185797X-RAY DIFFRACTION98.4542
7.834-55.050.202260.177456X-RAY DIFFRACTION97.7688

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