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- PDB-7kb6: Co-crystal structure of alpha glucosidase with compound 7 -

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Basic information

Entry
Database: PDB / ID: 7kb6
TitleCo-crystal structure of alpha glucosidase with compound 7
Components
  • Glucosidase 2 subunit beta
  • Isoform 2 of Neutral alpha-glucosidase AB
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Inhibitor complex
Function / homology
Function and homology information


mannosyl-oligosaccharide alpha-1,3-glucosidase / glucosidase II complex / nitrogen cycle metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / negative regulation of neuron projection development / in utero embryonic development / intracellular membrane-bounded organelle ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucosidase II complex / nitrogen cycle metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / negative regulation of neuron projection development / in utero embryonic development / intracellular membrane-bounded organelle / calcium ion binding / protein-containing complex binding / endoplasmic reticulum / RNA binding
Similarity search - Function
Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / EF hand / Endoplasmic reticulum targeting sequence. ...Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / EF hand / Endoplasmic reticulum targeting sequence. / LDL receptor-like superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-XOD / Glucosidase 2 subunit beta / Isoform 2 of Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarade, S.S. / Mariuzza, R.A.
CitationJournal: J.Med.Chem. / Year: 2021
Title: N-Substituted Valiolamine Derivatives as Potent Inhibitors of Endoplasmic Reticulum alpha-Glucosidases I and II with Antiviral Activity.
Authors: Karade, S.S. / Hill, M.L. / Kiappes, J.L. / Manne, R. / Aakula, B. / Zitzmann, N. / Warfield, K.L. / Treston, A.M. / Mariuzza, R.A.
History
DepositionOct 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
C: Isoform 2 of Neutral alpha-glucosidase AB
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,04690
Polymers345,9234
Non-polymers8,12386
Water15,799877
1
A: Isoform 2 of Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,35949
Polymers172,9612
Non-polymers4,39847
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Isoform 2 of Neutral alpha-glucosidase AB
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,68641
Polymers172,9612
Non-polymers3,72539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.909, 102.909, 239.827
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Isoform 2 of Neutral alpha-glucosidase AB / Alpha-glucosidase 2 / Glucosidase II subunit alpha


Mass: 110654.062 Da / Num. of mol.: 2 / Mutation: N97D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8BHN3-2, mannosyl-oligosaccharide alpha-1,3-glucosidase
#2: Protein Glucosidase 2 subunit beta / 80K-H protein / Glucosidase II subunit beta / Protein kinase C substrate 60.1 kDa protein heavy chain / PKCSH


Mass: 62307.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcsh / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08795

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Non-polymers , 8 types, 963 molecules

#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-XOD / (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(pyrimidin-2-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol


Mass: 491.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H33N5O7 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09M NPS, 0.1M Buffer system 1 pH 7.0, 29.0%v/v P500MME_P20K (Morpheus screen, condition C1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2020 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→44.56 Å / Num. obs: 140562 / % possible obs: 97.47 % / Redundancy: 6.4 % / Biso Wilson estimate: 38.09 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1286 / Rpim(I) all: 0.0524 / Rrim(I) all: 0.1392 / Net I/σ(I): 9.2
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.9757 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 13540 / CC1/2: 0.654 / CC star: 0.889 / Rpim(I) all: 0.4064 / Rrim(I) all: 1.06 / % possible all: 93.75

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000v717.1data reduction
HKL-2000v717.1data scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0E

5f0e


Resolution: 2.2→44.56 Å / SU ML: 0.2552 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.7639
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1935 1958 1.39 %
Rwork0.1666 138564 -
obs0.167 140522 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14804 0 518 881 16203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003415787
X-RAY DIFFRACTIONf_angle_d0.687621366
X-RAY DIFFRACTIONf_chiral_restr0.04682227
X-RAY DIFFRACTIONf_plane_restr0.00432762
X-RAY DIFFRACTIONf_dihedral_angle_d17.93145714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.33011240.26279498X-RAY DIFFRACTION93.37
2.26-2.320.28771430.23749574X-RAY DIFFRACTION94.56
2.32-2.380.26761290.21549643X-RAY DIFFRACTION94.96
2.38-2.460.2841430.21269678X-RAY DIFFRACTION95.28
2.46-2.550.25271360.21379713X-RAY DIFFRACTION95.63
2.55-2.650.24471510.19779834X-RAY DIFFRACTION96.71
2.65-2.770.27721310.18759950X-RAY DIFFRACTION97.61
2.77-2.920.22681470.20049952X-RAY DIFFRACTION98.6
2.92-3.10.20261510.179910086X-RAY DIFFRACTION99.11
3.1-3.340.20651360.164210076X-RAY DIFFRACTION99.39
3.34-3.680.17251380.152710197X-RAY DIFFRACTION99.91
3.68-4.210.15521460.142210103X-RAY DIFFRACTION99.98
4.21-5.30.13781320.126210129X-RAY DIFFRACTION99.92
5.3-44.560.16141510.154310131X-RAY DIFFRACTION99.68

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