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- PDB-8ekn: Co-crystal structure of Chaetomium glucosidase with compound 15 -

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Basic information

Entry
Database: PDB / ID: 8ekn
TitleCo-crystal structure of Chaetomium glucosidase with compound 15
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-WLQ / Mannosyl-oligosaccharide glucosidase
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKarade, S.S. / Mariuzza, R.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionSep 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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: Chaetomium alpha glucosidase
B: Chaetomium alpha glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,45319
Polymers186,6402
Non-polymers2,81417
Water7,350408
1
A: Chaetomium alpha glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,98511
Polymers93,3201
Non-polymers1,66610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaetomium alpha glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4688
Polymers93,3201
Non-polymers1,1487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.875, 179.332, 179.833
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.) Thermochaetoides thermophila (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
#5: 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 , 4 types, 424 molecules

#2: Chemical ChemComp-WLQ / (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{[4-({[(5P)-3-methyl-5-(pyridazin-3-yl)phenyl]amino}methyl)phenyl]methyl}piperidine-3,4,5-triol


Mass: 450.530 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H30N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.93 Å3/Da / Density % sol: 58.09 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2021
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.29→46.83 Å / Num. obs: 97615 / % possible obs: 99.36 % / Redundancy: 8.9 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.03868 / Net I/σ(I): 9.75
Reflection shellResolution: 2.29→2.375 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.9202 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 9205 / CC1/2: 0.797 / CC star: 0.942 / Rpim(I) all: 0.3355 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7T6W

7t6w


Resolution: 2.29→46.83 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.671 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 4944 5.1 %RANDOM
Rwork0.1881 ---
obs0.1905 92672 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.56 Å2 / Biso mean: 38.904 Å2 / Biso min: 19.65 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å2-0 Å20 Å2
2--0.11 Å20 Å2
3----2.35 Å2
Refinement stepCycle: final / Resolution: 2.29→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12149 0 180 409 12738
Biso mean--57.47 40.08 -
Num. residues----1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01312690
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711173
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.65517285
X-RAY DIFFRACTIONr_angle_other_deg1.3631.58525873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3651528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.822.324680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.115151940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.131573
X-RAY DIFFRACTIONr_chiral_restr0.0850.21570
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022847
LS refinement shellResolution: 2.293→2.353 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 299 -
Rwork0.287 6396 -
all-6695 -
obs--92.92 %

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