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6pm9

Crystal structure of the core catalytic domain of human O-GlcNAcase bound to MK-8719

Method: X-RAY DIFFRACTION Dmax: 112.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

O-GlcNAcase TIM-barrel domain

Homo sapiens

UniProt O60502

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 14–400 Chain B； UniProt 14–400 Chain F； UniProt 554–705 Chain G； UniProt 554–705 Not recorded OQ1 (3aR,5S,6S,7R,7aR)-5-(difluoromethyl)-2-(ethylamino)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M K-Na-tartrate tetrahydrate, 20% (w/v) PEG 3350 Resolution 2.86 Å R-free 0.309
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 14–400 Chain D； UniProt 14–400 Chain E； UniProt 554–705 Chain H； UniProt 554–705 Not recorded OQ1 (3aR,5S,6S,7R,7aR)-5-(difluoromethyl)-2-(ethylamino)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M K-Na-tartrate tetrahydrate, 20% (w/v) PEG 3350 Resolution 2.86 Å R-free 0.309

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6PM9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2YDQ CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide Deposited 2011-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 402–408（7 aa） Fragment：HOGA O-GLCNAC PEPTIDE, RESIDUES 402-408
Not recorded CD CADMIUM ION × 19 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.6M NAAC, 0.175M CDSO4, 0.1M HEPES PH 7.5
Resolution 2.60 Å R-free 0.231
5M7R Structure of human O-GlcNAc hydrolase Deposited 2016-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–916（916 aa）
Chain B 1–916（916 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；292 K；0.14 - 0.2 M triammonium citrate pH 7.5, 16-20 % PEG 3350
Resolution 2.35 Å R-free 0.249
5M7S Structure of human O-GlcNAc hydrolase with bound transition state analog ThiametG Deposited 2016-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–916（916 aa）
Chain B 1–916（916 aa）
Not recorded NHT (3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；292 K；0.1-0.2 M tri ammonium citrate pH 7.5 16-20 % PEG 3350
Resolution 2.40 Å R-free 0.232
5M7T Structure of human O-GlcNAc hydrolase with PugNAc type inhibitor Deposited 2016-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–916（916 aa）
Chain B 1–916（916 aa）
Not recorded GDV (5R,6R,7R,8S)-8-(ACETYLAMINO)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-N-PHENYL-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-2-CARBOXAMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；292 K；0.1-0.2 M tri Ammonium citrate 16-20 % PEG 3350
Resolution 2.60 Å R-free 0.235
5M7U Structure of human O-GlcNAc hydrolase with new iminocyclitol type inhibitor Deposited 2016-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–916（916 aa）
Chain B 1–916（916 aa）
Not recorded XHA 2-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-[3-[3-(trifluoromethyl)phenyl]propyl]pyrrolidin-2-yl]-~{N}-methyl-ethanamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；292 K；0.1-0.2 M tri Ammonium citrate pH 7.5 16-20 % PEG 3350
Resolution 2.30 Å R-free 0.227
5TKE Crystal Structure of Eukaryotic Hydrolase Deposited 2016-10-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 60–400（341 aa） Fragment：unp residues 60-542; unp residues 553-704
Chain A 553–704（152 aa） Fragment：unp residues 60-542; unp residues 553-704
Chain B 60–400（341 aa） Fragment：unp residues 60-542; unp residues 553-704
Chain B 553–704（152 aa） Fragment：unp residues 60-542; unp residues 553-704
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；293 K；0.032 M ammonium citrate tribasic (pH 7.0), 0.02 M MES monohydrate, 0.016 M imidazole, 0.002 M zinc sulfate heptahydrate, 0.128 M potassium thiocyanate, 12.8% w/v polyethylene glycol 3,350, 3.2% w/v polyethylene glycol monomethyl ether 2,000, and 5% w/v polyethylene glycol monomethyl ether 550
Resolution 2.48 Å R-free 0.236
5UHK Crystal structure of the core catalytic domain of Human O-GlcNAcase Deposited 2017-01-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 56–400（345 aa）
Chain B 544–705（162 aa）
Chain C 56–400（345 aa）
Chain D 544–705（162 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；14-17% PEG 3350, 0.2 M Mg Formate
Resolution 2.97 Å R-free 0.251
5UHL Crystal structure of the core catalytic domain of human O-GlcNAcase complexed with Thiamet G Deposited 2017-01-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 56–400（345 aa）
Chain B 544–705（162 aa）
Chain C 56–400（345 aa）
Chain D 544–705（162 aa）
Not recorded 8BJ (2Z,3aR,5R,6S,7R,7aR)-2-(ethylimino)-5-(hydroxymethyl)hexahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；14-17% PEG 3350, 0.2 M Mg Formate
Resolution 3.14 Å R-free 0.257
5UHO Crystal structure of the core catalytic domain of human O-GlcNAcase complexed with PUGNAc Deposited 2017-01-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 56–400（345 aa）
Chain B 544–705（162 aa）
Chain C 56–400（345 aa）
Chain D 544–705（162 aa）
Not recorded OAN O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；14-17% PEG 3350, 0.2 M Mg Formate
Resolution 3.21 Å R-free 0.259
5UHP Crystal structure of the core catalytic domain of human O-GlcNAcase Deposited 2017-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 14–400（387 aa）
Chain B 14–400（387 aa）
Chain F 554–705（152 aa）
Chain G 554–705（152 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M K Na tartrate tetrahydrate, 20% PEG 3350
Resolution 2.79 Å R-free 0.292
5UHP Crystal structure of the core catalytic domain of human O-GlcNAcase Deposited 2017-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 14–400（387 aa）
Chain D 14–400（387 aa）
Chain E 554–705（152 aa）
Chain H 554–705（152 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M K Na tartrate tetrahydrate, 20% PEG 3350
Resolution 2.79 Å R-free 0.292
5UN8 Crystal Structure of human O-GlcNAcase in complex with glycopeptide p53 Deposited 2017-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 60–400（341 aa） Fragment：UNP residues 60-400 and 553-704
Chain A 553–704（152 aa） Fragment：UNP residues 60-400 and 553-704
Chain C 60–400（341 aa） Fragment：UNP residues 60-400 and 553-704
Chain C 553–704（152 aa） Fragment：UNP residues 60-400 and 553-704
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；0.032 M ammonium citrate tribasic (pH 7.0), 0.02 M MES monohydrate, 0.016 M imidazole, 0.002 M zinc sulfate heptahydrate, 0.128 M potassium thiocyanate, 12.8% w/v polyethylene glycol 3,350, 3.2% w/v polyethylene glycol monomethyl ether 2,000, and 5% w/v polyethylene glycol monomethyl ether 550.
Resolution 2.13 Å R-free 0.229
5UN8 Crystal Structure of human O-GlcNAcase in complex with glycopeptide p53 Deposited 2017-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 60–400（341 aa） Fragment：UNP residues 60-400 and 553-704
Chain B 553–704（152 aa） Fragment：UNP residues 60-400 and 553-704
Chain D 60–400（341 aa） Fragment：UNP residues 60-400 and 553-704
Chain D 553–704（152 aa） Fragment：UNP residues 60-400 and 553-704
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；0.032 M ammonium citrate tribasic (pH 7.0), 0.02 M MES monohydrate, 0.016 M imidazole, 0.002 M zinc sulfate heptahydrate, 0.128 M potassium thiocyanate, 12.8% w/v polyethylene glycol 3,350, 3.2% w/v polyethylene glycol monomethyl ether 2,000, and 5% w/v polyethylene glycol monomethyl ether 550.
Resolution 2.13 Å R-free 0.229
5UN9 The crystal structure of human O-GlcNAcase in complex with Thiamet-G Deposited 2017-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 60–400（341 aa） Fragment：UNP residues 60-400 and 553-704
Chain A 553–704（152 aa） Fragment：UNP residues 60-400 and 553-704
Chain B 60–400（341 aa） Fragment：UNP residues 60-400 and 553-704
Chain B 553–704（152 aa） Fragment：UNP residues 60-400 and 553-704
Not recorded NHT (3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；0.128 M potassium thiocyanate, 0.032 M ammonium citrate tribasic (pH 7.0), 0.016 M imidazole (pH 7.0), 0.002 M zinc sulfate heptahydrate, 0.02 M MES monohydrate (pH 6.5), 12.8% w/v polyethylene glycol 3,350, 3.2% w/v polyethylene glycol monomethyl ether 2,000, 5% v/v polyethylene glycol monomethyl ether 550
Resolution 2.50 Å R-free 0.260
5VVO Structural Investigations of the Substrate Specificity of Human O-GlcNAcase Deposited 2017-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 60–400（341 aa） Fragment：UNP residues 60-400, 553-704
Chain A 553–704（152 aa） Fragment：UNP residues 60-400, 553-704
Chain B 60–400（341 aa） Fragment：UNP residues 60-400, 553-704
Chain B 553–704（152 aa） Fragment：UNP residues 60-400, 553-704
Mutation：D175N Mutation：D175N Mutation：D175N Mutation：D175N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550
Resolution 2.60 Å R-free 0.259
5VVT Structural Investigations of the Substrate Specificity of Human O-GlcNAcase Deposited 2017-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 60–400（341 aa）
Chain A 553–704（152 aa）
Chain C 60–400（341 aa）
Chain C 553–704（152 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550
Resolution 2.80 Å R-free 0.291
5VVU Structural Investigations of the Substrate Specificity of Human O-GlcNAcase Deposited 2017-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 60–400（341 aa） Fragment：UNP residues 60-400, 553-704
Chain A 553–704（152 aa） Fragment：UNP residues 60-400, 553-704
Chain C 60–400（341 aa） Fragment：UNP residues 60-400, 553-704
Chain C 553–704（152 aa） Fragment：UNP residues 60-400, 553-704
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550
Resolution 2.70 Å R-free 0.275
5VVV Structural Investigations of the Substrate Specificity of Human O-GlcNAcase Deposited 2017-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 60–400（341 aa） Fragment：UNP residues 60-400, 553-704
Chain A 553–704（152 aa） Fragment：UNP residues 60-400, 553-704
Chain C 60–400（341 aa） Fragment：UNP residues 60-400, 553-704
Chain C 553–704（152 aa） Fragment：UNP residues 60-400, 553-704
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550
Resolution 2.80 Å R-free 0.257
5VVX Structural Investigations of the Substrate Specificity of Human O-GlcNAcase Deposited 2017-05-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 60–400（341 aa） Fragment：UNP residues 60-400, 553-704
Chain A 553–704（152 aa） Fragment：UNP residues 60-400, 553-704
Chain C 60–400（341 aa） Fragment：UNP residues 60-400, 553-704
Chain C 553–704（152 aa） Fragment：UNP residues 60-400, 553-704
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550
Resolution 2.90 Å R-free 0.282
6HKI Crystal structure of surface entropy mutant of human O-GlcNAc hydrolase Deposited 2018-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–916（916 aa）
Chain B 1–916（916 aa）
Mutation：E602A, E605A Mutation：E602A, E605A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2 M sodium citrate tribasic, 17% polyethylene glycol 3350
Resolution 3.30 Å R-free 0.234
7OU6 Human O-GlcNAc hydrolase in complex with DNJNAc-thiazolidines Deposited 2021-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain AAA 1–916（916 aa）
Chain BBB 1–916（916 aa）
Not recorded 1XI ~{N}-[(3~{Z},6~{S},7~{R},8~{R},8~{a}~{S})-7,8-bis(oxidanyl)-3-(phenylmethyl)imino-1,5,6,7,8,8~{a}-hexahydro-[1,3]thiazolo[3,4-a]pyridin-6-yl]ethanamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；0.14 - 0.2 M triammonium citrate pH 7.5, 16-20 % PEG 3350
Resolution 2.41 Å R-free 0.271
7YEH Cryo-EM structure of human OGT-OGA complex Deposited 2022-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–916（916 aa）
Chain D 1–916（916 aa）
Not recorded UDP URIDINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
8P0L Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide Deposited 2023-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–916（916 aa）
Chain B 1–916（916 aa）
Not recorded CYS CYSTEINE × 1 SER SERINE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.14 - 0.2 M triammonium citrate pH 7.5, 16-20 % PEG 3350
Resolution 2.50 Å R-free 0.271
9BA8 O-GlcNAcase (OGA) inhibitor complex for the Treatment of Alzheimer's Disease Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 55–713（659 aa）
Chain B 55–713（659 aa）
Not recorded A1AKM N-[4-fluoro-5-({(2S,4S)-2-methyl-4-[(5-methyl-1,2,4-oxadiazol-3-yl)methoxy]piperidin-1-yl}methyl)-1,3-thiazol-2-yl]acetamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；15% PEG 3350, 200mM Magnesium Chloride, 100mM Hepes pH 7.0, 5% DMSO
Resolution 2.54 Å R-free 0.231
9BA9 O-GlcNAcase (OGA) inhibitor complex for the Treatment of Alzheimer's Disease Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 55–713（659 aa）
Not recorded A1AKL N-{5-[(piperidin-1-yl)methyl]-1,3-thiazol-2-yl}acetamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；33% PEG 300, 100mM Hepes pH 8.5
Resolution 2.75 Å R-free 0.260
9NE2 cryoEM structure of the human OGA-L Catalytic Dimer Deposited 2025-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–916（916 aa）
Chain B 1–916（916 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.63 Å
9NE4 cryoEM structure of the A-chain of the human OGA-L Catalytic Dimer Deposited 2025-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–916（916 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9NE5 cryoEM structure of the B-chain of the human OGA-L Catalytic Dimer Deposited 2025-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–916（916 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9QEN Cryo-EM structure of human O-GlcNAcase Deposited 2025-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 11–420（410 aa）
Chain A 553–916（364 aa）
Chain B 11–420（410 aa）
Chain B 553–916（364 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å

27 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OGA_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 2–388； UniProt 14–400 Author chain B； PDBConstruct 2–388； UniProt 14–400 Author chain C； PDBConstruct 2–388； UniProt 14–400 Author chain D； PDBConstruct 2–388； UniProt 14–400 Author chain E； PDBConstruct 2–153； UniProt 554–705 Author chain F； PDBConstruct 2–153； UniProt 554–705 Author chain G； PDBConstruct 2–153； UniProt 554–705 Author chain H； PDBConstruct 2–153； UniProt 554–705

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6pm9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6pm9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6pm9
Deposition date deposition_date2019-07-01
Structure title titleCrystal structure of the core catalytic domain of human O-GlcNAcase bound to MK-8719
Keywords keywordsHYDROLASE, O-GLCNACASE, GH84, INHIBITOR; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.94 Å
Radius of gyration Rg (electron density) rg_electron36.94 Å
Forward intensity I(0) i0554210000.00
Molecular weight molecular_weight197040.0 kDa
Excluded volume excluded_volume248480 ų
Envelope volume envelope_volume328760 ų
Hydration-shell volume shell_volume70940 ų
Envelope diameter envelope_diameter116.9 Å
Shell Rg shell_rg45.92 Å
Envelope Rg envelope_rg35.65 Å
Shape Rg shape_rg36.91 Å
Total Rg total_rg37.61 Å
Total atoms total_atoms13881
Residues n_residues1688
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.7 Å
Rg (real space) rg_real37.59 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real5.5420e+08
I(0) uncertainty (real space) i0_real_error7.5070e+06
Rg (reciprocal space) rg_reciprocal37.81 Å
I(0) (reciprocal space) i0_reciprocal554300000.0000
Solution quality estimate total_estimate0.9009
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.7 Å
Skewness Skewness skewness-0.026
Kurtosis Kurtosis kurtosis-0.592
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha134900000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.944
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6pm9A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id6pm9B00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id6pm9C00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id6pm9D00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
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8. Citations (1)

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9. Files and Curves (10)