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- PDB-7k41: Bacterial O-GlcNAcase (OGA) with compound -

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Basic information

Entry
Database: PDB / ID: 7k41
TitleBacterial O-GlcNAcase (OGA) with compound
ComponentsO-GlcNAcase BT_4395
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / OGA / virtual screening / structure based drug design / SBDD / TRANSFERASE / TRANSFERASE-TRANSFERASE 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 / identical protein binding
Similarity search - Function
: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 ...: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-VUA / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLane, W. / Tjhen, R. / Snell, G. / Sang, B.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of a Novel and Brain-Penetrant O -GlcNAcase Inhibitor via Virtual Screening, Structure-Based Analysis, and Rational Lead Optimization.
Authors: Tawada, M. / Fushimi, M. / Masuda, K. / Sun, H. / Uchiyama, N. / Kosugi, Y. / Lane, W. / Tjhen, R. / Endo, S. / Koike, T.
History
DepositionSep 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-GlcNAcase BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,55214
Polymers82,5171
Non-polymers1,03513
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.771, 52.646, 84.464
Angle α, β, γ (deg.)90.000, 99.693, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2779-

HOH

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Components

#1: Protein O-GlcNAcase BT_4395 / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Hexosaminidase B ...Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Hexosaminidase B / N-acetyl-beta-glucosaminidase


Mass: 82517.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Bacteroides thetaiotaomicron (bacteria) / References: UniProt: Q89ZI2, protein O-GlcNAcase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-VUA / 4-(4-methylpiperidin-1-yl)-N-(2-phenylethyl)pyrimidin-2-amine


Mass: 296.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5 M NaAcetate, 15% PEG 3350, 0.1 M MES pH 6.0, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→41.63 Å / Num. obs: 52607 / % possible obs: 93.41 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05266 / Net I/σ(I): 17.46
Reflection shellResolution: 2→2.064 Å / Rmerge(I) obs: 0.4469 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3250 / CC1/2: 0.781 / % possible all: 58.42

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CHN

2chn


Resolution: 2→41.63 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.531 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2183 2673 5.082 %
Rwork0.186 49929 -
all0.188 --
obs-52602 93.432 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.748 Å2
Baniso -1Baniso -2Baniso -3
1-0.848 Å2-0 Å2-2.838 Å2
2---1.759 Å20 Å2
3---1.776 Å2
Refinement stepCycle: LAST / Resolution: 2→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4759 0 70 154 4983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124953
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.656701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60223.745267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97315829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8121522
X-RAY DIFFRACTIONr_chiral_restr0.0970.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023876
X-RAY DIFFRACTIONr_nbd_refined0.2140.22278
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2233
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0590.25
X-RAY DIFFRACTIONr_mcbond_it1.2072.7372364
X-RAY DIFFRACTIONr_mcangle_it1.9764.0942950
X-RAY DIFFRACTIONr_scbond_it1.6162.8912589
X-RAY DIFFRACTIONr_scangle_it2.524.2423749
X-RAY DIFFRACTIONr_lrange_it4.95237.0467585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.993-2.0450.3411170.3332152X-RAY DIFFRACTION54.9395
2.045-2.1010.2741600.3012797X-RAY DIFFRACTION73.9065
2.101-2.1610.3291800.2893233X-RAY DIFFRACTION87.1553
2.161-2.2280.2771970.2523439X-RAY DIFFRACTION95.4581
2.228-2.3010.2881800.2243461X-RAY DIFFRACTION99.1288
2.301-2.3810.282120.2193367X-RAY DIFFRACTION99.7214
2.381-2.4710.251560.2033264X-RAY DIFFRACTION99.7085
2.471-2.5710.2261570.1933162X-RAY DIFFRACTION99.9398
2.571-2.6850.2031500.1983032X-RAY DIFFRACTION99.9058
2.685-2.8160.2681670.22884X-RAY DIFFRACTION100
2.816-2.9670.1871320.1842784X-RAY DIFFRACTION100
2.967-3.1470.1971420.1822596X-RAY DIFFRACTION100
3.147-3.3630.2181130.1822468X-RAY DIFFRACTION100
3.363-3.630.2181200.1742303X-RAY DIFFRACTION100
3.63-3.9740.193970.1592145X-RAY DIFFRACTION100
3.974-4.4390.159910.1541925X-RAY DIFFRACTION100
4.439-5.1180.2161060.1541692X-RAY DIFFRACTION99.9444
5.118-6.2470.206810.1891456X-RAY DIFFRACTION99.935
6.247-8.7510.2760.1631130X-RAY DIFFRACTION99.9172
8.751-41.6640.194390.174638X-RAY DIFFRACTION93.8974
Refinement TLS params.Method: refined / Origin x: -19.4176 Å / Origin y: -2.4944 Å / Origin z: 15.4681 Å
111213212223313233
T0.0236 Å20.041 Å20.0005 Å2-0.0918 Å20.002 Å2--0.0216 Å2
L2.372 °20.7648 °21.4347 °2-1.1959 °20.6197 °2--2.0473 °2
S0.0772 Å °0.263 Å °-0.1517 Å °-0.0367 Å °0.079 Å °-0.0096 Å °0.0668 Å °0.1619 Å °-0.1562 Å °
Refinement TLS groupSelection: ALL

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