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- PDB-7rev: Co-crystal structure of Chaetomium glucosidase with compound 3 -

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Basic information

Entry
Database: PDB / ID: 7rev
TitleCo-crystal structure of Chaetomium glucosidase with compound 3
ComponentsChaetomium alpha glucosidase
KeywordsHYDROLASE/INHIBITOR / alpha glucosidase I / Hydrolase / Inhibitor complex / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


mannosyl-oligosaccharide glucosidase / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / protein N-linked glycosylation / endoplasmic reticulum membrane
Similarity search - Function
Glycosyl hydrolase family 63, C-terminal / Glycosyl hydrolase family 63, N-terminal / Glycosyl hydrolase family 63, N-terminal domain superfamily / Glycosyl hydrolase family 63 C-terminal domain / Glycosyl hydrolase family 63 N-terminal domain / Glycoside hydrolase family 63 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Chem-5RK / Mannosyl-oligosaccharide glucosidase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKarade, S.S. / Mariuzza, R.A.
CitationJournal: J.Med.Chem. / Year: 2023
Title: Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum alpha-Glucosidase I with Anti-SARS-CoV-2 Activity.
Authors: Karade, S.S. / Franco, E.J. / Rojas, A.C. / Hanrahan, K.C. / Kolesnikov, A. / Yu, W. / MacKerell Jr., A.D. / Hill, D.C. / Weber, D.J. / Brown, A.N. / Treston, A.M. / Mariuzza, R.A.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: 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 1.2Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaetomium alpha glucosidase
B: Chaetomium alpha glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,61613
Polymers186,6402
Non-polymers1,97611
Water4,594255
1
A: Chaetomium alpha glucosidase
hetero molecules


  • defined by author
  • 94 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)93,9504
Polymers93,3201
Non-polymers6313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaetomium alpha glucosidase
hetero molecules


  • defined by author
  • 94.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)94,6659
Polymers93,3201
Non-polymers1,3458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.365, 178.090, 179.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Chaetomium alpha glucosidase


Mass: 93319.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061620 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human) / References: UniProt: G0SFD1
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 265 molecules

#2: Chemical ChemComp-5RK / (2R,3R,4R,5S)-1-[(4-{[4-(furan-2-yl)-2-methylanilino]methyl}phenyl)methyl]-2-(hydroxymethyl)piperidine-3,4,5-triol


Mass: 438.516 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H30N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 Bis Tris pH 6.5, 1.6-2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2021
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: 2.3→46.72 Å / Num. obs: 95691 / % possible obs: 99.58 % / Redundancy: 6.4 % / CC1/2: 0.983 / CC star: 0.996 / Rpim(I) all: 0.101 / Rrim(I) all: 0.2572 / Rsym value: 0.236 / Net I/σ(I): 6.26
Reflection shellResolution: 2.3→2.384 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.44 / Num. unique obs: 9157 / CC1/2: 0.52 / CC star: 0.827 / Rpim(I) all: 0.677 / % possible all: 96.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-2000v717.1data reduction
HKL-2000v717.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J5T

4j5t


Resolution: 2.3→46.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.599 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 4774 5 %RANDOM
Rwork0.1908 ---
obs0.1932 90917 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.02 Å2 / Biso mean: 40.652 Å2 / Biso min: 19.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å20 Å2-0 Å2
2--0.49 Å20 Å2
3----2.96 Å2
Refinement stepCycle: final / Resolution: 2.3→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12144 0 128 257 12529
Biso mean--59.02 40.39 -
Num. residues----1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01212661
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.64517253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99151536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61922.335681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.791151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4071573
X-RAY DIFFRACTIONr_chiral_restr0.1140.21562
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029975
LS refinement shellResolution: 2.302→2.362 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 319 -
Rwork0.3 6392 -
all-6711 -
obs--95.61 %

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