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- PDB-11lh: OgOGA IN COMPLEX WITH LIGAND 7 -

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Basic information

Entry
Database: PDB / ID: 11lh
TitleOgOGA IN COMPLEX WITH LIGAND 7
ComponentsProtein O-GlcNAcase
KeywordsHYDROLASE/INHIBITOR / GLYCOSIDE HYDROLASE / INHIBITOR / HYDROLASE / HYDROLASE-INHIBITOR Complex
Function / homology
Function and homology information


protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Protein O-GlcNAcase
Similarity search - Component
Biological speciesOceanicola granulosus HTCC2516 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsShaffer, P.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Discovery of 5‐Azaindole Inhibitors of O‐GlcNAcase for the Treatment of Alzheimer's Disease and Related Tauopathies.
Authors: Bouton, J. / Bretteville, A. / Tresadern, G. / Shaffer, P. / Austin, N. / Buijnsters, P. / Cedervall, E.P. / Darville, N. / Fonteyn, I. / Leenaerts, J. / Lamenca, C.M. / Mertens, L. / ...Authors: Bouton, J. / Bretteville, A. / Tresadern, G. / Shaffer, P. / Austin, N. / Buijnsters, P. / Cedervall, E.P. / Darville, N. / Fonteyn, I. / Leenaerts, J. / Lamenca, C.M. / Mertens, L. / Peeters, D. / Velter, A.I. / Roosbroeck, Y.V. / Ebneth, A. / Bartolome, J.M. / Trabanco, A.A. / Oehlrich, D.
History
DepositionMar 3, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 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: Protein O-GlcNAcase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5532
Polymers50,2431
Non-polymers3101
Water90150
1
A: Protein O-GlcNAcase
hetero molecules

A: Protein O-GlcNAcase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1064
Polymers100,4852
Non-polymers6202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)84.672, 96.349, 62.430
Angle α, β, γ (deg.)90.00, 106.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein O-GlcNAcase / OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / N-acetyl- ...OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / N-acetyl-beta-D-glucosaminidase / N-acetyl-beta-glucosaminidase


Mass: 50242.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanicola granulosus HTCC2516 (bacteria)
Strain: HTCC2516 / Gene: OG2516_04129 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2CEE3, protein O-GlcNAcase
#2: Chemical ChemComp-A1DE4 / N~4~-butyl-N~2~-(2,6-dichlorophenyl)pyridine-2,4-diamine


Mass: 310.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17Cl2N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.75
Details: 22% (w/v) PEG4K, 0.15 M MgCl2, 0.1 Tris/HCl pH 8.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.44→62.15 Å / Num. obs: 17213 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.099 / Net I/σ(I): 7.42
Reflection shellResolution: 2.44→2.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.485 / Num. unique obs: 4377 / CC1/2: 0.808 / Rrim(I) all: 0.598 / % possible all: 96.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→62.15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.88 / SU B: 34.135 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R: 0.654 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30107 1061 6.2 %RANDOM
Rwork0.21563 ---
obs0.22088 16152 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4 Å20 Å2-0.57 Å2
2--6.99 Å20 Å2
3----2.28 Å2
Refinement stepCycle: LAST / Resolution: 2.44→62.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 20 50 3521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193484
X-RAY DIFFRACTIONr_bond_other_d0.0030.023233
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9534762
X-RAY DIFFRACTIONr_angle_other_deg1.48937364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90522.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39815489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0781534
X-RAY DIFFRACTIONr_chiral_restr0.0820.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214030
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02847
X-RAY DIFFRACTIONr_mcbond_it4.6256.0921755
X-RAY DIFFRACTIONr_mcbond_other4.6246.0931754
X-RAY DIFFRACTIONr_mcangle_it6.05510.282192
X-RAY DIFFRACTIONr_mcangle_other6.05510.282193
X-RAY DIFFRACTIONr_scbond_it5.2736.3791729
X-RAY DIFFRACTIONr_scbond_other5.2576.3791729
X-RAY DIFFRACTIONr_scangle_other6.89510.6192571
X-RAY DIFFRACTIONr_long_range_B_refined7.58655.0073777
X-RAY DIFFRACTIONr_long_range_B_other7.58554.9983777
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 78 -
Rwork0.332 1117 -
obs--90.46 %
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)
13.11060.35610.41031.1056-0.39762.31260.0233-0.1544-0.26810.0732-0.04880.02230.16940.42440.02550.08860.0550.01570.10360.02060.160214.6929.29131.395
25.27571.1231-0.70830.4069-0.62482.4429-0.11071.09-0.2335-0.1540.1936-0.01060.1553-0.0808-0.08290.15520.0222-0.010.2392-0.05220.1079-4.23712.469.194
31.3248-1.59140.04776.1211-1.161.670.15820.45260.1235-0.0547-0.19710.3598-0.4185-0.19440.03890.19120.0665-0.01010.2380.04040.1705-14.8527.74310.067
410.9108-0.4201-11.33791.19592.066715.4914-0.2773-0.4801-0.63370.51150.1761-0.53480.3411.05590.10120.7971-0.0549-0.01580.45080.09640.6453-13.29739.84219.589
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 280
2X-RAY DIFFRACTION2A281 - 323
3X-RAY DIFFRACTION3A324 - 420
4X-RAY DIFFRACTION4A421 - 999

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