7khv

CpOGA IN COMPLEX WITH LIGAND 54

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	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 CALCIUM ION × 1 SULFATE ION × 11 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	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 CALCIUM ION × 1 SULFATE ION × 15 CHLORIDE ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	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 CALCIUM ION × 1 SULFATE ION × 9 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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 Author chain C； PDBConstruct 1–594； UniProt 31–624 Author chain D； PDBConstruct 1–594； UniProt 31–624 Author chain E； PDBConstruct 1–594； UniProt 31–624 Author chain F； 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	7khv
Deposition date deposition_date	2020-10-22
Structure title title	CpOGA IN COMPLEX WITH LIGAND 54
Keywords keywords	GLYCOSIDE HYDROLASE, INHIBITOR, HYDROLASE, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7khv__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7khv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7khv__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	38.37 Å
Rg (electron density)	37.90 Å
Total Rg	38.18 Å
Atom count	18278
Residues	1171
Excluded volume	164800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7khv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7khv__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7khv__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	O-GlcNAcase NagJ
Molecular weight formula_weight	66692.7 kDa
EC 编号 ec_number	3.2.1.169
Mutation mutation	D298N, V331C, N388D
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	55791

VGPKTGEENQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDNIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITCPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI

Source Source

Source organism organism	Clostridium perfringens
NCBI taxonomy ID ncbi_taxonomy_id	1502
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	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
Molecular weight formula_weight	398.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	35

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1565

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (17 domains)

Domain ID domain_id	d7khva1
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	d7khva2
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	d7khva3
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	d7khvb1
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	d7khvb2
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	d7khvb3
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	d7khvc1
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	d7khvc2
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	d7khvc3
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	d7khvd1
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	d7khvd2
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	d7khvd3
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	d7khve1
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	d7khve2
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	d7khve3
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	d7khvf1
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	d7khvf2
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

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Unit-cell length a length_a	149.489 Å
Unit-cell length b length_b	178.104 Å
Unit-cell length c length_c	407.054 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	203.530 Å
R factor r_factor	0.2067
R_work r_work	0.2065
R_free r_free	0.2471

CpOGA IN COMPLEX WITH LIGAND 54

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7khv__assembly_1__model_1

7khv__assembly_1__model_1 | I(q)

7khv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (17 domains)

7. Citations (1)

CpOGA IN COMPLEX WITH LIGAND 54

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7khv__assembly_1__model_1

7khv__assembly_1__model_1 | I(q)

7khv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (17 domains)

7. Citations (1)