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- PDB-11lj: Human OGA IN COMPLEX WITH LIGAND 24 -

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Basic information

Entry
Database: PDB / ID: 11lj
TitleHuman OGA IN COMPLEX WITH LIGAND 24
Components
  • Protein O-GlcNAcase 535-704 Peptide
  • Protein O-GlcNAcase N-Terminal Fragment
KeywordsHYDROLASE/INHIBITOR / GLYCOSIDE HYDROLASE / INHIBITOR / HYDROLASE / HYDROLASE-INHIBITOR Complex
Function / homology
Function and homology information


hyalurononglucosaminidase activity / glycoprotein metabolic process / hexosaminidase activity / N-acetylglucosamine metabolic process / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / glycoprotein catabolic process / protein O-linked glycosylation / membrane ...hyalurononglucosaminidase activity / glycoprotein metabolic process / hexosaminidase activity / N-acetylglucosamine metabolic process / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / glycoprotein catabolic process / protein O-linked glycosylation / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Acyl-CoA N-acyltransferase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Protein O-GlcNAcase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.325 Å
AuthorsShaffer, P.L. / Cedervall, P.
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 N-Terminal Fragment
C: Protein O-GlcNAcase 535-704 Peptide
B: Protein O-GlcNAcase N-Terminal Fragment
D: Protein O-GlcNAcase 535-704 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9088
Polymers126,1254
Non-polymers7834
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-93 kcal/mol
Surface area34850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.838, 96.838, 257.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein O-GlcNAcase N-Terminal Fragment / OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma- ...OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma-expressed antigen 5 / N-acetyl-beta-D-glucosaminidase / N-acetyl-beta-glucosaminidase / Nuclear cytoplasmic O-GlcNAcase and acetyltransferase / NCOAT


Mass: 43505.945 Da / Num. of mol.: 2 / Fragment: residues 11-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGA, HEXC, KIAA0679, MEA5, MGEA5 / Production host: Escherichia coli (E. coli) / References: UniProt: O60502, protein O-GlcNAcase
#2: Protein Protein O-GlcNAcase 535-704 Peptide / OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma- ...OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma-expressed antigen 5 / N-acetyl-beta-D-glucosaminidase / N-acetyl-beta-glucosaminidase / Nuclear cytoplasmic O-GlcNAcase and acetyltransferase / NCOAT


Mass: 19556.377 Da / Num. of mol.: 2 / Fragment: residues 535-704
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGA, HEXC, KIAA0679, MEA5, MGEA5 / Production host: Escherichia coli (E. coli) / References: UniProt: O60502, protein O-GlcNAcase
#3: Chemical ChemComp-A1DE3 / N,N-dimethyl-2-(4-{[4-methyl-2-(propan-2-yl)pyridin-3-yl]amino}-1H-pyrrolo[3,2-c]pyridin-1-yl)acetamide


Mass: 351.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 6-20% (w/v) PEG-3350, 0.2M Calcium Acetate, 0.01M Barium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.325→60.436 Å / Num. obs: 37403 / % possible obs: 93.8 % / Redundancy: 13 % / CC1/2: 0.998 / Rpim(I) all: 0.054 / Net I/σ(I): 10.6
Reflection shellResolution: 2.325→2.59 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1870 / CC1/2: 0.739 / Rpim(I) all: 0.536 / % possible all: 69.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACTdata extraction
XDS20190315data reduction
STARANISO1.0.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.325→60.436 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / Phase error: 35.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 1846 4.94 %
Rwork0.2233 --
obs0.2255 37395 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.325→60.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6966 0 54 51 7071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027209
X-RAY DIFFRACTIONf_angle_d0.4429763
X-RAY DIFFRACTIONf_dihedral_angle_d17.9824252
X-RAY DIFFRACTIONf_chiral_restr0.0371024
X-RAY DIFFRACTIONf_plane_restr0.0031251
LS refinement shellResolution: 2.325→2.41 Å
RfactorNum. reflection% reflection
Rfree0.3484 16 -
Rwork0.3174 328 -
obs--8 %
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)
14.460.99230.36322.41481.92313.9552-0.08430.0476-0.4825-0.05570.0940.15010.3654-0.2197-0.01810.3352-0.0867-0.02730.13390.02630.2614-66.5089-11.4132-20.8942
22.75020.9788-0.13382.27610.43333.82590.0891-0.34120.14650.1631-0.19430.5289-0.3371-0.43450.12540.28290.0156-0.0110.3024-0.05390.1941-68.74582.0709-11.7894
32.7341-0.0498-1.58091.892-1.04012.42240.1062-0.3933-0.49450.2721-0.1827-0.36440.79520.7946-0.22580.6103-0.0322-0.28620.8793-0.23750.1738-29.84151.4992-10.923
41.3707-0.3774-0.07120.94060.54421.53630.1744-0.49860.84760.1202-0.0368-0.4561-0.70220.7408-0.08640.7172-0.23110.04820.7176-0.23750.7088-39.617716.5902-18.3679
53.2871-0.32880.09513.2706-0.79822.9949-0.192-0.012-0.55220.05620.08970.04050.1067-0.13910.07430.32360.0985-0.01210.1095-0.07510.2371-34.3362-9.1957-37.2081
65.85031.24392.00772.2819-0.13933.7082-0.2281-0.7984-0.57290.5183-0.0808-0.13650.13060.11780.17630.52430.2537-0.05590.41310.07170.432-25.4808-14.0931-28.9956
74.75661.7210.3884.5935-0.75671.7615-0.2013-0.48510.090.4353-0.0947-0.3551-0.18210.14530.2160.52910.1975-0.11660.2650.03360.6428-17.3499-11.4835-28.6298
83.7606-0.74580.23397.5041-1.56564.818-0.21820.0138-0.45880.30710.0955-1.3340.22251.0280.12180.34710.0879-0.08560.3769-0.07950.7182-11.7578-8.65-35.4939
94.7262-0.70490.65122.7504-0.18422.4389-0.1180.34660.9920.1074-0.1634-0.9093-0.51430.17950.11720.3174-0.015-0.12370.1381-0.02770.4243-23.38535.4264-41.5671
105.5392-0.86030.74681.2825-0.04912.4610.09350.54-0.4501-0.3193-0.1499-0.04210.0131-0.33670.05860.42830.0641-0.09280.2672-0.05880.1244-49.0777-0.074-47.5678
113.6795-0.29480.22572.86940.44431.53890.21610.15050.70140.1193-0.22960.1063-0.6519-0.22310.03530.55510.089-0.00760.28310.01320.3425-58.037716.8379-37.6268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 392 )
3X-RAY DIFFRACTION3chain 'A' and resid 393 through chain 'C' and resid 564
4X-RAY DIFFRACTION4chain 'C' and (resid 565 through 694 )
5X-RAY DIFFRACTION5chain 'B' and (resid 59 through 103 )
6X-RAY DIFFRACTION6chain 'B' and (resid 104 through 147 )
7X-RAY DIFFRACTION7chain 'B' and (resid 148 through 190 )
8X-RAY DIFFRACTION8chain 'B' and (resid 191 through 215 )
9X-RAY DIFFRACTION9chain 'B' and (resid 216 through 317 )
10X-RAY DIFFRACTION10chain 'B' and resid 318 through chain 'D' and resid 572
11X-RAY DIFFRACTION11chain 'D' and (resid 573 through 692 )

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