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- PDB-7kad: Co-crystal structure of alpha glucosidase with compound 6 -

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Basic information

Entry
Database: PDB / ID: 7kad
TitleCo-crystal structure of alpha glucosidase with compound 6
Components
  • Glucosidase 2 subunit betaGlucosidases
  • Isoform 2 of Neutral alpha-glucosidase AB
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Hydrolases / Inhibitor complex
Function / homology
Function and homology information


mannosyl-oligosaccharide alpha-1,3-glucosidase / glucosidase II complex / 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 ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucosidase II complex / 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 / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / 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 / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / 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-W9Y / 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: 2.506 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
DepositionSep 30, 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

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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)352,81676
Polymers345,9234
Non-polymers6,89372
Water8,161453
1
A: Isoform 2 of Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,90644
Polymers172,9612
Non-polymers3,94442
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)175,91032
Polymers172,9612
Non-polymers2,94930
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.689, 102.689, 240.275
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 33 through 53 or (resid 54...
21(chain C and (resid 33 through 34 or (resid 35...
12(chain B and (resid 31 through 77 or (resid 78...
22(chain D and (resid 31 through 58 or (resid 59...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 33 through 53 or (resid 54...A33 - 53
121(chain A and (resid 33 through 53 or (resid 54...A54
131(chain A and (resid 33 through 53 or (resid 54...A33 - 966
141(chain A and (resid 33 through 53 or (resid 54...A33 - 966
151(chain A and (resid 33 through 53 or (resid 54...A33 - 966
161(chain A and (resid 33 through 53 or (resid 54...A33 - 966
211(chain C and (resid 33 through 34 or (resid 35...C33 - 34
221(chain C and (resid 33 through 34 or (resid 35...C35
231(chain C and (resid 33 through 34 or (resid 35...C33 - 966
241(chain C and (resid 33 through 34 or (resid 35...C33 - 966
251(chain C and (resid 33 through 34 or (resid 35...C33 - 966
261(chain C and (resid 33 through 34 or (resid 35...C33 - 966
112(chain B and (resid 31 through 77 or (resid 78...B31 - 77
122(chain B and (resid 31 through 77 or (resid 78...B78 - 80
132(chain B and (resid 31 through 77 or (resid 78...B31 - 401
142(chain B and (resid 31 through 77 or (resid 78...B31 - 401
152(chain B and (resid 31 through 77 or (resid 78...B31 - 401
162(chain B and (resid 31 through 77 or (resid 78...B31 - 401
212(chain D and (resid 31 through 58 or (resid 59...D31 - 58
222(chain D and (resid 31 through 58 or (resid 59...D59
232(chain D and (resid 31 through 58 or (resid 59...D31 - 201
242(chain D and (resid 31 through 58 or (resid 59...D31 - 201
252(chain D and (resid 31 through 58 or (resid 59...D31 - 201
262(chain D and (resid 31 through 58 or (resid 59...D31 - 201

NCS ensembles :
ID
1
2

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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 / Glucosidases / 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): Espi-HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08795

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Non-polymers , 8 types, 525 molecules

#3: Chemical ChemComp-W9Y / (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(1H-1,2,3-triazol-1-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol


Mass: 480.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32N6O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / 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 / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09M NPS, 0.1M Buffer system 1 pH 7.0, 29%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: 2.506→42.277 Å / Num. obs: 97233 / % possible obs: 99.92 % / Redundancy: 8.4 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1507 / Rpim(I) all: 0.05497 / Rrim(I) all: 0.1605 / Net I/σ(I): 8.42
Reflection shellResolution: 2.506→2.596 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 9617 / CC1/2: 0.613 / CC star: 0.872 / Rpim(I) all: 0.4061 / Rrim(I) all: 1.194 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
HKL-2000v717.1data reduction
HKL-2000v717.1data scaling
PHENIX1.14_3228phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0E

5f0e


Resolution: 2.506→42.277 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 2036 2.09 %
Rwork0.1723 95197 -
obs0.173 97233 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.75 Å2 / Biso mean: 51.043 Å2 / Biso min: 20.06 Å2
Refinement stepCycle: final / Resolution: 2.506→42.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14968 0 433 453 15854
Biso mean--71.45 49.1 -
Num. residues----1885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315908
X-RAY DIFFRACTIONf_angle_d0.65121566
X-RAY DIFFRACTIONf_dihedral_angle_d15.0849346
X-RAY DIFFRACTIONf_chiral_restr0.0462243
X-RAY DIFFRACTIONf_plane_restr0.0042784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8158X-RAY DIFFRACTION6.653TORSIONAL
12C8158X-RAY DIFFRACTION6.653TORSIONAL
21B782X-RAY DIFFRACTION6.653TORSIONAL
22D782X-RAY DIFFRACTION6.653TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.506-2.56410.31451400.25926311
2.5641-2.62820.3151240.23856397
2.6282-2.69920.30471380.21976345
2.6992-2.77860.2391320.21416350
2.7786-2.86830.25651320.20996351
2.8683-2.97080.24731320.21236329
2.9708-3.08970.26131360.19546327
3.0897-3.23030.23451380.18946379
3.2303-3.40050.21561400.18266348
3.4005-3.61350.19521360.16816336
3.6135-3.89230.18641380.15946356
3.8923-4.28360.16721340.14696376
4.2836-4.90270.15231400.1366318
4.9027-6.17380.18021350.15716328
6.1738-42.2770.18161410.16336346

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