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- PDB-11tn: Candida glabrata Glycogen Debranching Enzyme (GDE) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 11tn
TitleCandida glabrata Glycogen Debranching Enzyme (GDE) in complex with Miglustat
ComponentsGlycogen debranching enzyme
KeywordsSUGAR BINDING PROTEIN / protein-ligand complex / Miglustat / GDE / Glycogen Debranching Enzyme
Function / homology
Function and homology information


amylo-alpha-1,6-glucosidase / amylo-alpha-1,6-glucosidase activity / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / glycogen biosynthetic process / glycogen catabolic process / cytoplasm
Similarity search - Function
Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, C-terminal / Glycogen debranching enzyme, glucanotransferase domain / Amylo-alpha-1,6-glucosidase / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme ...Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, C-terminal / Glycogen debranching enzyme, glucanotransferase domain / Amylo-alpha-1,6-glucosidase / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-NBV / Glycogen debranching enzyme
Similarity search - Component
Biological speciesNakaseomyces glabratus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.236 Å
AuthorsMishra, N. / Paz, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R01GM149871-02S1 United States
CitationJournal: To Be Published
Title: Off-target binding of Miglustat to glycogen debranching enzyme
Authors: Barber, D. / Mishra, N. / Hegarty, F. / Paz, A.
History
DepositionMar 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 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: Glycogen debranching enzyme
B: Glycogen debranching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,5304
Polymers348,0922
Non-polymers4392
Water00
1
A: Glycogen debranching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,2652
Polymers174,0461
Non-polymers2191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycogen debranching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,2652
Polymers174,0461
Non-polymers2191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.078, 199.274, 254.213
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 5 - 1528 / Label seq-ID: 1 - 1524

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Glycogen debranching enzyme / Glycogen debrancher


Mass: 174045.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nakaseomyces glabratus (fungus) / Gene: GDB1, CAGL0G09977g / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6FSK0, 4-alpha-glucanotransferase, amylo-alpha-1,6-glucosidase
#2: Chemical ChemComp-NBV / (2R,3R,4R,5S)-1-BUTYL-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL


Mass: 219.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H21NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
Has ligand of interestY
Has protein modificationN

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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: 57.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MES (pH 7), 7% v/v Tacsimate (pH 7), 20% w/v PEG MME 5K

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→127.106 Å / Num. obs: 64558 / % possible obs: 93.5 % / Redundancy: 14.2 % / Biso Wilson estimate: 60.61 Å2 / CC1/2: 0.98 / Net I/σ(I): 6.2
Reflection shellResolution: 3.236→3.595 Å / Num. unique obs: 36604 / CC1/2: 0.527

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.105)refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.236→127.106 Å / Cor.coef. Fo:Fc: 0.825 / Cor.coef. Fo:Fc free: 0.839 / Cross valid method: THROUGHOUT
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 1857 5.073 %RANDOM
Rwork0.2354 34748 --
all0.237 ---
obs-36605 56.69 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 86.576 Å2
Baniso -1Baniso -2Baniso -3
1--6.919 Å2-0 Å2-0 Å2
2--2.002 Å2-0 Å2
3---4.916 Å2
Refinement stepCycle: LAST / Resolution: 3.236→127.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23443 0 30 0 23473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01224067
X-RAY DIFFRACTIONr_bond_other_d0.0010.01622282
X-RAY DIFFRACTIONr_angle_refined_deg0.8581.82432635
X-RAY DIFFRACTIONr_angle_other_deg0.3331.76751461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21352908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.2335145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.037104093
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.683101174
X-RAY DIFFRACTIONr_chiral_restr0.0440.23493
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0228399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025627
X-RAY DIFFRACTIONr_nbd_refined0.1870.25728
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.223746
X-RAY DIFFRACTIONr_nbtor_refined0.1760.212014
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.211983
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2570
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1240.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.217
X-RAY DIFFRACTIONr_nbd_other0.1010.2131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.23
X-RAY DIFFRACTIONr_mcbond_it1.921611644
X-RAY DIFFRACTIONr_mcbond_other1.92611644
X-RAY DIFFRACTIONr_mcangle_it3.39110.78814548
X-RAY DIFFRACTIONr_mcangle_other3.39210.78914549
X-RAY DIFFRACTIONr_scbond_it1.6176.11512423
X-RAY DIFFRACTIONr_scbond_other1.6176.11512424
X-RAY DIFFRACTIONr_scangle_it2.99911.21518087
X-RAY DIFFRACTIONr_scangle_other2.99911.21518088
X-RAY DIFFRACTIONr_lrange_it7.8471.651101906
X-RAY DIFFRACTIONr_lrange_other7.8471.651101907
X-RAY DIFFRACTIONr_ncsr_local_group_10.1250.0544828
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.125150.05012
12BX-RAY DIFFRACTIONLocal ncs0.125150.05012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.236-3.320.31238X-RAY DIFFRACTION
3.32-3.4110.388160.365223X-RAY DIFFRACTION5.1945
3.411-3.5090.382370.357660X-RAY DIFFRACTION15.5096
3.509-3.6170.368460.3371076X-RAY DIFFRACTION25.8287
3.617-3.7360.362880.3121487X-RAY DIFFRACTION37.1638
3.736-3.8670.316840.2991781X-RAY DIFFRACTION45.3551
3.867-4.0130.3131020.2731902X-RAY DIFFRACTION50.9017
4.013-4.1760.2881160.2562148X-RAY DIFFRACTION59.7204
4.176-4.3620.2841240.2422317X-RAY DIFFRACTION66.6212
4.362-4.5750.2571080.2162447X-RAY DIFFRACTION73.1882
4.575-4.8220.2281640.2152519X-RAY DIFFRACTION80.1374
4.822-5.1140.2221550.2112578X-RAY DIFFRACTION87.0659
5.114-5.4660.2541410.2172600X-RAY DIFFRACTION91.8874
5.466-5.9030.3041350.2342578X-RAY DIFFRACTION97.6602
5.903-6.4650.3441130.2322457X-RAY DIFFRACTION100
6.465-7.2260.2881170.2112207X-RAY DIFFRACTION100
7.226-8.3390.277980.1831973X-RAY DIFFRACTION100
8.339-10.2030.2021040.1671653X-RAY DIFFRACTION100
10.203-14.3830.226780.1921324X-RAY DIFFRACTION100
14.383-127.1060.403310.424780X-RAY DIFFRACTION99.1443
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6644-0.1479-0.16160.60610.10760.64750.07260.19920.0027-0.2341-0.0679-0.0506-0.12160.1238-0.00470.3565-0.05010.11290.1332-0.00880.0584-49.2429-6.096636.3153
20.2991-0.1307-0.1080.41330.22460.6330.14720.0750.0002-0.1886-0.016-0.04830.00780.022-0.13120.28470.0373-0.04880.0235-0.01410.076711.300411.621637.0996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA5 - 1605
2X-RAY DIFFRACTION2ALLB5 - 1605

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