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- PDB-9elb: Structure of glucocerebrosidase in complex with a covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 9elb
TitleStructure of glucocerebrosidase in complex with a covalent inhibitor
ComponentsGlucosylceramidase
KeywordsHYDROLASE/INHIBITOR / glucocerebrosidase / cerezyme / Gaucher disease / glycoside hydrolase / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of macromolecule metabolic process / steryl-beta-glucosidase activity / galactosylceramidase activity / glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / glucosyltransferase activity / lysosome organization / regulation of protein catabolic process / regulation of TOR signaling ...negative regulation of macromolecule metabolic process / steryl-beta-glucosidase activity / galactosylceramidase activity / glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / glucosyltransferase activity / lysosome organization / regulation of protein catabolic process / regulation of TOR signaling / cholesterol metabolic process / regulation of macroautophagy / protein catabolic process / regulation of membrane potential / autophagy / signaling receptor binding / lysosomal membrane
Similarity search - Function
Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04355 Canada
CitationJournal: To Be Published
Title: Irreversible inhibitors and activity-based probes, derived from an adaptable conduritol aziridine scaffold, for studying glucocerebrosidase and GBA2 in vitro and in vivo
Authors: Wang, S. / Tavassoly, O. / Chowdhury, M.A. / Carter, L. / Brown, D. / Bravo, R.C. / Zhang, Z. / Tesolin, D. / Quartey, M.A. / Pluvinage, B. / Nyarko, J.N. / Kumar, M. / Feldman, R.A. / ...Authors: Wang, S. / Tavassoly, O. / Chowdhury, M.A. / Carter, L. / Brown, D. / Bravo, R.C. / Zhang, Z. / Tesolin, D. / Quartey, M.A. / Pluvinage, B. / Nyarko, J.N. / Kumar, M. / Feldman, R.A. / Boraston, A.B. / Mousseau, D.D. / van der Spoel, A.C. / Phenix, C.P.
History
DepositionDec 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosylceramidase
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,79443
Polymers111,2802
Non-polymers4,51341
Water7,134396
1
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,84822
Polymers55,6401
Non-polymers2,20821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,94521
Polymers55,6401
Non-polymers2,30520
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.870, 284.907, 91.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1099-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucosylceramidase / Glucocerebrosidase


Mass: 55640.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified (others) / References: UniProt: B2R6A7, glucosylceramidase

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Sugars , 2 types, 5 molecules

#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.: 2
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
#4: 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.: 3 / Source method: obtained synthetically / 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, 432 molecules

#3: Chemical ChemComp-A1BLU / (1S,2R,3R,4S,5S)-5-(octylamino)cyclohexane-1,2,3,4-tetrol


Mass: 275.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H29NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 5.0, 1.6 M ammonium sulfate, and 3% (w/v) sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 57054 / % possible obs: 99.6 % / Redundancy: 4.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.038 / Net I/σ(I): 14.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2554 / CC1/2: 0.921 / Rpim(I) all: 0.223 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.96 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 2729 4.92 %
Rwork0.2075 --
obs0.2096 55507 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7729 0 268 396 8393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038206
X-RAY DIFFRACTIONf_angle_d0.55611159
X-RAY DIFFRACTIONf_dihedral_angle_d15.9851136
X-RAY DIFFRACTIONf_chiral_restr0.0421240
X-RAY DIFFRACTIONf_plane_restr0.0041408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.25561490.22712554X-RAY DIFFRACTION91
2.44-2.490.281360.22452721X-RAY DIFFRACTION96
2.49-2.540.281350.22262784X-RAY DIFFRACTION98
2.54-2.590.30231300.23242799X-RAY DIFFRACTION98
2.59-2.650.26981420.23682824X-RAY DIFFRACTION99
2.65-2.720.29591420.22072823X-RAY DIFFRACTION99
2.72-2.790.29081340.23612823X-RAY DIFFRACTION99
2.79-2.880.29281520.23542841X-RAY DIFFRACTION99
2.88-2.970.27251580.23432780X-RAY DIFFRACTION99
2.97-3.080.26561330.22792822X-RAY DIFFRACTION99
3.08-3.20.30461400.23032821X-RAY DIFFRACTION99
3.2-3.340.28991490.23272788X-RAY DIFFRACTION98
3.34-3.520.32311160.24822520X-RAY DIFFRACTION87
3.52-3.740.34241620.27822623X-RAY DIFFRACTION93
3.74-4.030.22231470.18882625X-RAY DIFFRACTION91
4.03-4.430.18931410.15812782X-RAY DIFFRACTION96
4.43-5.070.15361510.14212878X-RAY DIFFRACTION99
5.07-6.380.18881590.17122915X-RAY DIFFRACTION100
6.38-29.960.21411530.18933055X-RAY DIFFRACTION100

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