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

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Basic information

Entry
Database: PDB / ID: 9elc
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: 2.2 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)116,44745
Polymers111,2802
Non-polymers5,16743
Water12,016667
1
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,14723
Polymers55,6401
Non-polymers2,50722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,30122
Polymers55,6401
Non-polymers2,66121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.359, 284.811, 91.590
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-1095-

HOH

21B-1326-

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 , 3 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: 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
#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.: 2
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, 705 molecules

#4: Chemical ChemComp-A1BLE / (1S,2R,3S,4S,5S)-5-(hexylamino)-4-(hexyloxy)cyclohexane-1,2,3-triol


Mass: 331.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 667 / 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: 3.23 Å3/Da / Density % sol: 61.96 %
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: 2.2→30 Å / Num. obs: 73304 / % possible obs: 99.3 % / Redundancy: 4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.042 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2124 / CC1/2: 0.81 / Rpim(I) all: 0.31

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.92 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 3631 5.1 %
Rwork0.1734 --
obs0.1753 71156 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7770 0 309 667 8746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048324
X-RAY DIFFRACTIONf_angle_d0.67611322
X-RAY DIFFRACTIONf_dihedral_angle_d17.1251165
X-RAY DIFFRACTIONf_chiral_restr0.0451254
X-RAY DIFFRACTIONf_plane_restr0.0051427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.25791180.20852124X-RAY DIFFRACTION80
2.23-2.260.26981290.20652196X-RAY DIFFRACTION84
2.26-2.290.27681330.21172295X-RAY DIFFRACTION87
2.29-2.330.27031280.20932357X-RAY DIFFRACTION89
2.33-2.360.2521450.21082447X-RAY DIFFRACTION93
2.36-2.40.25941430.2092500X-RAY DIFFRACTION94
2.4-2.440.24151320.19922548X-RAY DIFFRACTION96
2.44-2.490.22281350.19912611X-RAY DIFFRACTION98
2.49-2.530.25761330.20192631X-RAY DIFFRACTION99
2.53-2.590.24091660.20532617X-RAY DIFFRACTION99
2.59-2.640.27031310.19612662X-RAY DIFFRACTION99
2.64-2.70.2291290.19622678X-RAY DIFFRACTION100
2.7-2.770.26281390.19052669X-RAY DIFFRACTION100
2.77-2.850.25461410.19672642X-RAY DIFFRACTION100
2.85-2.930.24821440.19822682X-RAY DIFFRACTION100
2.93-3.020.2271270.19622680X-RAY DIFFRACTION100
3.02-3.130.26161380.18982690X-RAY DIFFRACTION100
3.13-3.260.23981550.17632667X-RAY DIFFRACTION100
3.26-3.410.17831510.16832676X-RAY DIFFRACTION100
3.41-3.580.19551510.16492673X-RAY DIFFRACTION100
3.58-3.810.18641550.14962696X-RAY DIFFRACTION100
3.81-4.10.15671420.14152689X-RAY DIFFRACTION99
4.1-4.510.16111510.13062698X-RAY DIFFRACTION100
4.51-5.160.14831420.13552730X-RAY DIFFRACTION100
5.16-6.490.21181410.16962779X-RAY DIFFRACTION100
6.49-29.920.21791320.18612888X-RAY DIFFRACTION100

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