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- PDB-7khs: OgOGA IN COMPLEX WITH LIGAND 55 -

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Basic information

Entry
Database: PDB / ID: 7khs
TitleOgOGA IN COMPLEX WITH LIGAND 55
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
Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-WG4 / Protein O-GlcNAcase
Similarity search - Component
Biological speciesOceanicola granulosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsShaffer, P.L.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Diazaspirononane Nonsaccharide Inhibitors of O-GlcNAcase (OGA) for the Treatment of Neurodegenerative Disorders.
Authors: Martinez-Viturro, C.M. / Trabanco, A.A. / Royes, J. / Fernandez, E. / Tresadern, G. / Vega, J.A. / Del Cerro, A. / Delgado, F. / Garcia Molina, A. / Tovar, F. / Shaffer, P. / Ebneth, A. / ...Authors: Martinez-Viturro, C.M. / Trabanco, A.A. / Royes, J. / Fernandez, E. / Tresadern, G. / Vega, J.A. / Del Cerro, A. / Delgado, F. / Garcia Molina, A. / Tovar, F. / Shaffer, P. / Ebneth, A. / Bretteville, A. / Mertens, L. / Somers, M. / Alonso, J.M. / Bartolome-Nebreda, J.M.
History
DepositionOct 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein O-GlcNAcase
B: Protein O-GlcNAcase
C: Protein O-GlcNAcase
D: Protein O-GlcNAcase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,75911
Polymers200,9714
Non-polymers1,7887
Water4,702261
1
A: Protein O-GlcNAcase
B: Protein O-GlcNAcase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3495
Polymers100,4852
Non-polymers8633
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-43 kcal/mol
Surface area34590 Å2
MethodPISA
2
C: Protein O-GlcNAcase
D: Protein O-GlcNAcase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4116
Polymers100,4852
Non-polymers9254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-36 kcal/mol
Surface area34410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.231, 83.076, 122.964
Angle α, β, γ (deg.)90.000, 90.250, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALAA1 - 4473 - 449
21METMETVALVALBB1 - 4473 - 449
12METMETVALVALAA1 - 4473 - 449
22METMETVALVALCC1 - 4473 - 449
13SERSERGLYGLYAA0 - 4462 - 448
23SERSERGLYGLYDD0 - 4462 - 448
14METMETVALVALBB1 - 4473 - 449
24METMETVALVALCC1 - 4473 - 449
15METMETVALVALBB1 - 4473 - 449
25METMETVALVALDD1 - 4473 - 449
16METMETVALVALCC1 - 4473 - 449
26METMETVALVALDD1 - 4473 - 449

NCS ensembles :
ID
1
2
3
4
5
6

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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.: 4 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanicola granulosus (bacteria) / Strain: ATCC BAA-861 / DSM 15982 / KCTC 12143 / HTCC2516 / Gene: OG2516_04129 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2CEE3, protein O-GlcNAcase
#2: Chemical
ChemComp-WG4 / N-(5-{[(5S)-7-(5-methylimidazo[1,2-a]pyrimidin-7-yl)-2,7-diazaspiro[4.4]nonan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide


Mass: 411.524 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H25N7OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.75 / Details: 22% PEG-4000, 0.15M MgCl2, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.625
11-h,-k,l20.375
ReflectionResolution: 1.78→44.79 Å / Num. obs: 176418 / % possible obs: 88.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 37.333 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.071 / Χ2: 1.048 / Net I/σ(I): 7.7
Reflection shellResolution: 1.78→2.04 Å / Redundancy: 2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 60543 / CC1/2: 0.681 / Rrim(I) all: 0.639 / % possible all: 94

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: previously solved O. granulosus O-GlcNAcase structure

Resolution: 1.78→44.79 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.897 / SU B: 4.619 / SU ML: 0.083 / SU R Cruickshank DPI: 0.0379 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2961 2533 1.4 %RANDOM
Rwork0.2731 ---
obs0.2734 173884 87.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.79 Å2 / Biso mean: 38.633 Å2 / Biso min: 8.47 Å2
Baniso -1Baniso -2Baniso -3
1-6.4 Å20 Å2-1.1 Å2
2---0.57 Å2-0 Å2
3----5.83 Å2
Refinement stepCycle: final / Resolution: 1.78→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13867 0 227 279 14373
Biso mean--30.5 29.47 -
Num. residues----1754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01914169
X-RAY DIFFRACTIONr_bond_other_d0.0040.0213080
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.95219368
X-RAY DIFFRACTIONr_angle_other_deg1.36329747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29751762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75522.412680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.356151975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.41415143
X-RAY DIFFRACTIONr_chiral_restr0.1020.22063
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116462
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023505
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A277340.05
12B277340.05
21A270060.05
22C270060.05
31A290160.05
32D290160.05
41B267940.04
42C267940.04
51B275360.04
52D275360.04
61C271320.04
62D271320.04
LS refinement shellResolution: 1.782→1.829 Å
RfactorNum. reflection% reflection
Rfree0.329 199 -
Rwork0.275 11532 -
obs--79.17 %
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)
10.93850.11090.06130.64290.33760.97750.0308-0.0415-0.02620.1519-0.0296-0.11770.11150.1794-0.00110.1178-0.0210.03280.19060.01440.305158.0440.387267.965
21.52740.69130.47372.95991.93674.19830.15730.17390.01080.00290.08140.0220.1308-0.2571-0.23870.0495-0.00510.07550.1767-0.00590.304430.603-4.504258.435
32.0932-0.2317-1.90780.29730.14392.6248-0.04410.0508-0.0090.04470.0211-0.02840.0781-0.05550.02310.0763-0.02880.05750.1372-0.0250.310320.966-13.131269.962
41.38810.67170.48092.4146-1.0230.9739-0.0085-0.3983-0.02960.2115-0.02850.021-0.1891-0.30030.0370.17330.00130.04160.3655-0.0670.387529.416-20.539284.469
50.89010.41630.04330.79710.45080.6484-0.01620.2249-0.0414-0.1948-0.03740.08910.0906-0.19120.05370.233-0.04380.0510.2744-0.04420.434832.788-39.903258.219
63.03570.4865-1.62011.16470.3681.74770.1551-0.2165-0.16650.3011-0.1513-0.12880.06540.2935-0.00380.1563-0.02160.02030.2777-0.00470.349853.304-33.62275.691
70.5571-0.311-1.10491.27950.58444.2797-0.006-0.27140.0240.32990.0083-0.1548-0.22360.1802-0.00240.1967-0.0444-0.01370.3350.00380.311449.245-21.622287.389
83.08711.70092.5641.04841.34562.57530.1816-0.3304-0.08890.2446-0.1348-0.0129-0.04130.0348-0.04670.2409-0.06020.10710.3509-0.00960.42233.027-12.832285.829
90.6059-0.2705-0.08270.7280.59270.6106-0.0781-0.2240.1704-0.025-0.07650.1003-0.2159-0.12470.15470.3598-0.0227-0.08360.3151-0.04250.544985.62855.147295.501
101.07881.67420.05032.72160.35940.7355-0.16660.01640.0841-0.35110.07040.1037-0.29160.21880.09620.3151-0.1046-0.01450.28570.07260.4531105.68548.947278.109
110.198-0.20390.04581.46750.16380.29630.03130.29130.113-0.3634-0.1808-0.0117-0.23090.16960.14950.2619-0.08570.02140.51130.09190.4395101.3437.068266.415
123.4525-1.86541.60992.364-0.95462.45590.27390.3513-0.1553-0.5864-0.11530.11430.05390.2726-0.15860.1998-0.06020.04680.2737-0.02730.35485.09328.474267.592
130.7746-0.2416-0.11290.43680.24250.5447-0.02510.0534-0.0082-0.03690.0046-0.0664-0.06130.14180.02060.1079-0.01230.06040.2124-0.00550.3089110.51614.636285.574
143.6255-0.533-0.10750.18470.05940.0276-0.0529-0.23430.10410.1610.02410.01850.0669-0.03440.02870.2248-0.01870.07960.2515-0.0230.357683.12919.286294.849
152.5894-0.01671.37081.1280.32530.974-0.1002-0.1712-0.0087-0.0410.05730.0267-0.1572-0.15240.04290.1238-0.01340.05330.1637-0.01670.303773.69428.332283.491
162.3005-0.8170.5410.3854-0.31752.13190.10670.14940.0897-0.1742-0.0616-0.0326-0.08570.2404-0.04510.2648-0.0709-0.00170.22450.00320.369481.51235.674268.802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 280
2X-RAY DIFFRACTION2A281 - 323
3X-RAY DIFFRACTION3A324 - 408
4X-RAY DIFFRACTION4A409 - 447
5X-RAY DIFFRACTION5B1 - 280
6X-RAY DIFFRACTION6B281 - 323
7X-RAY DIFFRACTION7B324 - 408
8X-RAY DIFFRACTION8B409 - 447
9X-RAY DIFFRACTION9C1 - 280
10X-RAY DIFFRACTION10C281 - 323
11X-RAY DIFFRACTION11C324 - 408
12X-RAY DIFFRACTION12C409 - 447
13X-RAY DIFFRACTION13D1 - 280
14X-RAY DIFFRACTION14D281 - 323
15X-RAY DIFFRACTION15D324 - 408
16X-RAY DIFFRACTION16D409 - 447

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