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- PDB-7rd2: Co-crystal structure of Chaetomium glucosidase with compound 2 -

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Basic information

Entry
Database: PDB / ID: 7rd2
TitleCo-crystal structure of Chaetomium glucosidase with compound 2
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-5X7 / Mannosyl-oligosaccharide glucosidase
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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
DepositionJul 9, 2021Deposition 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 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)189,34218
Polymers186,6402
Non-polymers2,70216
Water66737
1
A: Chaetomium alpha glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,60510
Polymers93,3201
Non-polymers1,2859
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaetomium alpha glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7378
Polymers93,3201
Non-polymers1,4177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.563, 178.393, 179.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 52 molecules

#3: Chemical ChemComp-5X7 / (2R,3R,4R,5S)-1-{[4-({4-[(2R,6S)-2,6-dimethylmorpholin-4-yl]-2-nitroanilino}methyl)phenyl]methyl}-2-(hydroxymethyl)piperidine-3,4,5-triol


Mass: 516.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H36N4O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.89 Å3/Da / Density % sol: 57.42 %
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 PILATUS3 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: 2.61→46.68 Å / Num. obs: 65663 / % possible obs: 99.74 % / Redundancy: 6.5 % / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.1805 / Rpim(I) all: 0.077 / Net I/σ(I): 7.96
Reflection shellResolution: 2.61→2.703 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 6397 / CC1/2: 0.555 / CC star: 0.845 / Rpim(I) all: 0.618 / % possible all: 98.07

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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: 7T6W

7t6w


Resolution: 2.61→46.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.634 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.457 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22891 3347 5.1 %RANDOM
Rwork0.17605 ---
obs0.17876 62340 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.427 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å2-0 Å20 Å2
2---0.65 Å20 Å2
3----3.61 Å2
Refinement stepCycle: 1 / Resolution: 2.61→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12136 0 168 37 12341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212663
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.64717260
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81451529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25322.324680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.332151926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8231573
X-RAY DIFFRACTIONr_chiral_restr0.1240.21563
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029943
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4375.1246116
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.4187.6787639
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.3595.466547
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.55897.63753771
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.61→2.676 Å
RfactorNum. reflection% reflection
Rfree0.353 246 -
Rwork0.327 4303 -
obs--94.99 %

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