SAXSdb — 2xpk

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 31–624 Chain B； UniProt 31–624	Fragment：RESIDUES 31-624 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 experimental conditions	Resolution 2.40 Å R-free 0.242

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 2XPK	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 mutation/modification Different ligand/ion 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 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 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 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 oligomeric state 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 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 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 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 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 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 mutation/modification 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
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 A 31–618（588 aa） Fragment：RESIDUES 31-618	Mutation：YES	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
2YDR CpOGA D298N in complex with p53-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 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 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 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 oligomeric state 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 oligomeric state 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 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 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 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 1–594； UniProt 31–624 Author chain B； PDBConstruct 1–594； UniProt 31–624

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	2xpk
Deposition date deposition_date	2010-08-26
Structure title title	Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases
Keywords keywords	HYDROLASE, SIGNALLING; HYDROLASE
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	39.11 Å
Radius of gyration Rg (electron density) rg_electron	38.81 Å
Forward intensity I(0) i0	271116000.00
Molecular weight molecular_weight	132100.0 kDa
Excluded volume excluded_volume	164030 Å³
Envelope volume envelope_volume	209660 Å³
Hydration-shell volume shell_volume	45846 Å³
Envelope diameter envelope_diameter	147.1 Å
Shell Rg shell_rg	43.64 Å
Envelope Rg envelope_rg	38.77 Å
Shape Rg shape_rg	38.82 Å
Total Rg total_rg	39.02 Å
Total atoms total_atoms	9309
Residues n_residues	1170
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	135.9 Å
Rg (real space) rg_real	39.41 Å
Rg uncertainty (real space) rg_real_error	1.45 Å
I(0) (real space) i0_real	2.7110e+08
I(0) uncertainty (real space) i0_real_error	5.0740e+06
Rg (reciprocal space) rg_reciprocal	39.23 Å
I(0) (reciprocal space) i0_reciprocal	271100000.0000
Solution quality estimate total_estimate	0.8488
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.4 Å
Skewness Skewness skewness	0.464
Kurtosis Kurtosis kurtosis	-0.397
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	40250000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.823; Smooth: 0.875

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	O-GLCNACASE NAGJ
Molecular weight formula_weight	66693.7 kDa
EC 编号 ec_number	3.2.1.52
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9771

VGPKTGEENQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITCPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI

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 non-polymer

Description description	;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 ;
Molecular weight formula_weight	391.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	460

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2xpka1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family family	d.92.2.0 — automated matches

Domain ID domain_id	d2xpka2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.10 — alpha-D-glucuronidase/Hyaluronidase catalytic domain

Domain ID domain_id	d2xpka3
Class class	a — All alpha proteins
Fold Fold fold	a.246 — Hyaluronidase domain-like
Superfamily Superfamily superfamily	a.246.1 — Hyaluronidase post-catalytic domain-like
Family Family family	a.246.1.0 — automated matches

Domain ID domain_id	d2xpkb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family family	d.92.2.0 — automated matches

Domain ID domain_id	d2xpkb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.10 — alpha-D-glucuronidase/Hyaluronidase catalytic domain

Domain ID domain_id	d2xpkb3
Class class	a — All alpha proteins
Fold Fold fold	a.246 — Hyaluronidase domain-like
Superfamily Superfamily superfamily	a.246.1 — Hyaluronidase post-catalytic domain-like
Family Family family	a.246.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2xpkA01
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	2xpkA02
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	2xpkA03
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

Domain ID domain_id	2xpkB01
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	2xpkB02
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	2xpkB03
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	130.145 Å
Unit-cell length b length_b	144.970 Å
Unit-cell length c length_c	153.061 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.020 Å
R factor r_factor	0.1961
R_work r_work	0.1956
R_free r_free	0.2423

fit	/app/data/saxs_computation/xp/2xpk/2xpk.fit
pddf	/app/data/pr_computation/xp/2xpk/2xpk.pr.out
profile	/app/data/saxs_computation/xp/2xpk/2xpk.dat

Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases

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

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