SAXSdb — 2ydq

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1. Protein Identity and Related Structures Protein Identity & Related Structures

O-GLCNACASE NAGJ

CLOSTRIDIUM PERFRINGENS

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 31–618	Fragment：RESIDUES 31-618 Mutation：YES	BIFUNCTIONAL PROTEIN NCOAT × 1 （O60502） 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

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 2YDQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2J62 Structure of a bacterial O-glcnacase in complex with glcnacstatin Deposited 2006-09-22	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 31–624（594 aa） Fragment：RESIDUES 31-624 Chain B 31–624（594 aa） Fragment：RESIDUES 31-624	Not recorded	CL CHLORIDE ION × 4 GSZ N-[(5R,6R,7R,8S)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDIN-8-YL]-2-METHYLPROPANAMIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.26 Å R-free 0.219
2JH2 X-ray crystal structure of a cohesin-like module from Clostridium perfringens Deposited 2007-02-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 768–909（142 aa） Fragment：RESIDUES 768-909	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.295
2JH2 X-ray crystal structure of a cohesin-like module from Clostridium perfringens Deposited 2007-02-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 768–909（142 aa） Fragment：RESIDUES 768-909	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.295
2JH2 X-ray crystal structure of a cohesin-like module from Clostridium perfringens Deposited 2007-02-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 768–909（142 aa） Fragment：RESIDUES 768-909	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.295
2O4E The solution structure of a protein-protein interaction module from a family 84 glycoside hydrolase of Clostridium perfringens Deposited 2006-12-04	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 768–909（142 aa） Fragment：Putative protein-protein interaction module	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Pressure 1 NMR sample composition 1mM U-15N,13C x82, 25mM hepes, 50mM nacl, 5mM cacl2, pH 7.0	Resolution not provided
2OZN The Cohesin-Dockerin Complex of NagJ and NagH from Clostridium perfringens Deposited 2007-02-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 768–909（142 aa） Fragment：Cohesin module (residues 768-909)	Not recorded	CL CHLORIDE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；21% (w/v) polyethylene glycol 2000, 0.2M ammonium sulfate, 100mM sodium acetate, pH 4.5	Resolution 1.60 Å R-free 0.246
2V5C Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure Deposited 2008-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–624（594 aa） Fragment：CATALYTIC MODULE, RESIDUES 31-624	Not recorded	CA CALCIUM ION × 2 CAC CACODYLATE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.255
2V5C Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure Deposited 2008-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–624（594 aa） Fragment：CATALYTIC MODULE, RESIDUES 31-624	Not recorded	CA CALCIUM ION × 2 CAC CACODYLATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.255
2V5D Structure of a Family 84 Glycoside Hydrolase and a Family 32 Carbohydrate-Binding Module in Tandem from Clostridium perfringens. Deposited 2008-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–767（737 aa） Fragment：RESIDUES 31-767	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.30 Å R-free 0.370
2VUR Chemical dissection of the link between Streptozotocin, O-GlcNAc and pancreatic cell death Deposited 2008-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–624（594 aa） Fragment：O-GLCNACASE DOMAIN, RESIDUES 31-624	Not recorded	YX1 2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.241
2VUR Chemical dissection of the link between Streptozotocin, O-GlcNAc and pancreatic cell death Deposited 2008-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–624（594 aa） Fragment：O-GLCNACASE DOMAIN, RESIDUES 31-624	Not recorded	YX1 2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.241
2WB5 GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation Deposited 2009-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–624（594 aa） Fragment：O-GLCNACASE DOMAIN, RESIDUES 31-624	Not recorded	CL CHLORIDE ION × 2 NA SODIUM ION × 1 VGB (5R,6R,7R,8S)-6,7-dihydroxy-5-(hydroxymethyl)-2-(2-phenylethyl)-8-(propanoylamino)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；30% PEG 8000, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM COCADYLATE, pH 6.5	Resolution 2.31 Å R-free 0.237
2WB5 GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation Deposited 2009-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–624（594 aa） Fragment：O-GLCNACASE DOMAIN, RESIDUES 31-624	Not recorded	CL CHLORIDE ION × 3 VGB (5R,6R,7R,8S)-6,7-dihydroxy-5-(hydroxymethyl)-2-(2-phenylethyl)-8-(propanoylamino)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；30% PEG 8000, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM COCADYLATE, pH 6.5	Resolution 2.31 Å R-free 0.237
2X0Y Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds Deposited 2009-12-18	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 31–624（594 aa） Fragment：RESIDUES 31-624 Chain B 31–624（594 aa） Fragment：RESIDUES 31-624	Not recorded	X0T 7-[(2S)-2,3-DIHYDROXYPROPYL]-1,3-DIMETHYL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30 % PEG 8000 AND GAMMA-BUTYROLACTONE	Resolution 2.25 Å R-free 0.246
2XPK Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases Deposited 2010-08-26	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 31–624（594 aa） Fragment：RESIDUES 31-624 Chain B 31–624（594 aa） Fragment：RESIDUES 31-624	Mutation：YES Mutation：YES	Z0M N-[(5R,6R,7R,8S)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDIN-8-YL]-3-SULFANYLPROPANAMIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.242
2YDR CpOGA D298N in complex with p53-derived O-GlcNAc peptide Deposited 2011-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 31–618（588 aa） Fragment：RESIDUES 31-618	Mutation：YES	CD CADMIUM ION × 18 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.6 M NAAC, 0.175 M CDSO4, 0.1 M HEPES PH 7.5	Resolution 2.75 Å R-free 0.219
2YDS CpOGA D298N in complex with TAB1-derived O-GlcNAc peptide Deposited 2011-03-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 31–618（588 aa） Fragment：RESIDUES 31-618	Mutation：YES	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 19	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.55 Å R-free 0.238
4ZXL CpOGA D298N in complex with Drosophila HCF -derived Thr-O-GlcNAc peptide Deposited 2015-05-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 39–617（579 aa） Fragment：UNP residues 39-617	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；CpOGA D298N was concentrated to 35 mg/ml in 25 mM Tris/HCl (pH 8.0) and crystallized from 0.175 M CdSO4 and 0.6 M sodium acetate pH 7.5	Resolution 2.60 Å R-free 0.220
5OXD Complex of a C. perfringens O-GlcNAcase with a fragment hit Deposited 2017-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–618（588 aa）	Not recorded	CD CADMIUM ION × 22 B2W 5-(trifluoromethyl)-2,3-dihydro-1~{H}-1,4-diazepine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Apo crystals were grown in 0.6 M NaAcetate pH 7.5, 0.175 M cadmium sulphate (ML). Crystals were then transferred into a drop supplemented with 10 mM ligand and incubated for 4 h. Crystals were cryo-protected by short immersion in ML supplemented with 20% glycerol and saturated with ligand.	Resolution 2.60 Å R-free 0.221
6RHE CpOGA D298N in complex with hOGA-derived S-GlcNAc peptide Deposited 2019-04-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 31–619（589 aa）	Mutation：D298N	CD CADMIUM ION × 25 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1:1 drops of proytein mixed with crystallisation buffer: 0.175 M CdSO4 and 0.6 M NaAc	Resolution 3.10 Å R-free 0.233
7KHV CpOGA IN COMPLEX WITH LIGAND 54 Deposited 2020-10-22	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 31–624（594 aa） Chain B 31–624（594 aa）	Mutation：D298N, V331C, N388D Mutation：D298N, V331C, N388D	X1A N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 11 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.6；293 K；2.4M Ammonium Sulfate, 0.1M Hepes	Resolution 2.30 Å R-free 0.247
7KHV CpOGA IN COMPLEX WITH LIGAND 54 Deposited 2020-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 31–624（594 aa） Chain D 31–624（594 aa）	Mutation：D298N, V331C, N388D Mutation：D298N, V331C, N388D	X1A N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 15 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.6；293 K；2.4M Ammonium Sulfate, 0.1M Hepes	Resolution 2.30 Å R-free 0.247
7KHV CpOGA IN COMPLEX WITH LIGAND 54 Deposited 2020-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 31–624（594 aa） Chain F 31–624（594 aa）	Mutation：D298N, V331C, N388D Mutation：D298N, V331C, N388D	X1A N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.6；293 K；2.4M Ammonium Sulfate, 0.1M Hepes	Resolution 2.30 Å R-free 0.247

16 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OGA_CLOP1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–590； UniProt 31–618

BIFUNCTIONAL PROTEIN NCOAT

OrganismNot specified

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain T； UniProt 402–408	Fragment：HOGA O-GLCNAC PEPTIDE, RESIDUES 402-408	O-GLCNACASE NAGJ × 1 （Q0TR53） 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

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 2YDQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 60-542; 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
6PM9 Crystal structure of the core catalytic domain of human O-GlcNAcase bound to MK-8719 Deposited 2019-07-01	Different construct Different mutation/modification Different oligomeric state 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	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
6PM9 Crystal structure of the core catalytic domain of human O-GlcNAcase bound to MK-8719 Deposited 2019-07-01	Different construct Different mutation/modification Different oligomeric state 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	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
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 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 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 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 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 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 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCOAT_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain T； PDBConstruct 1–7； UniProt 402–408

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ydq
Deposition date deposition_date	2011-03-24
Structure title title	CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide
Keywords keywords	HYDROLASE-PEPTIDE COMPLEX; HYDROLASE/PEPTIDE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.91 Å
Radius of gyration Rg (electron density) rg_electron	26.72 Å
Forward intensity I(0) i0	84401100.00
Molecular weight molecular_weight	67824.0 kDa
Excluded volume excluded_volume	82306 Å³
Envelope volume envelope_volume	98398 Å³
Hydration-shell volume shell_volume	31261 Å³
Envelope diameter envelope_diameter	95.1 Å
Shell Rg shell_rg	33.41 Å
Envelope Rg envelope_rg	27.34 Å
Shape Rg shape_rg	26.54 Å
Total Rg total_rg	27.83 Å
Total atoms total_atoms	4649
Residues n_residues	586
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	91.4 Å
Rg (real space) rg_real	27.92 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	8.4400e+07
I(0) uncertainty (real space) i0_real_error	1.0880e+06
Rg (reciprocal space) rg_reciprocal	27.92 Å
I(0) (reciprocal space) i0_reciprocal	84400000.0000
Solution quality estimate total_estimate	0.8935
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.5 Å
Skewness Skewness skewness	0.347
Kurtosis Kurtosis kurtosis	-0.386
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16270000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	O-GLCNACASE NAGJ
Molecular weight formula_weight	66130.0 kDa
EC 编号 ec_number	3.2.1.52
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4753

GSVGPKTGEENQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDNIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALS

来源 Source

来源生物 organism	CLOSTRIDIUM PERFRINGENS
NCBI Class编号 ncbi_taxonomy_id	1502
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	BIFUNCTIONAL PROTEIN NCOAT
Molecular weight formula_weight	670.8 kDa
EC 编号 ec_number	3.2.1.169
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

VAHSGAK

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2ydqA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	379 — Chitobiase; domain 2
Homologous superfamily homologous superfamily	10 — Chitobiase/beta-hexosaminidase domain 2-like

Domain ID domain_id	2ydqA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	2ydqA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	460 — Hyaluronidase post-catalytic domain-like

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8. Citations (1)

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Unit-cell length a length_a	118.210 Å
Unit-cell length b length_b	118.210 Å
Unit-cell length c length_c	148.210 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	24.700 Å
R factor r_factor	0.1938
R_work r_work	0.1930
R_free r_free	0.2305

fit	/app/data/saxs_computation/yd/2ydq/2ydq.fit
pddf	/app/data/pr_computation/yd/2ydq/2ydq.pr.out
profile	/app/data/saxs_computation/yd/2ydq/2ydq.dat

CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

O-GLCNACASE NAGJ

State in the Current Structure

Other States of the Same Protein in the Database

BIFUNCTIONAL PROTEIN NCOAT

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)