2jiw

Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with 2- Acetylamino-2-deoxy-1-epivalienamine

Method: X-RAY DIFFRACTION

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

O-GLCNACASE BT_4395

BACTEROIDES THETAIOTAOMICRON

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	N-[(1S,2R,5R,6R)-2-AMINO-5,6-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOHEX-3-EN-1-YL]ACETAMIDE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N-[(1S,2R,5R,6R)-2-AMINO-5,6-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOHEX-3-EN-1-YL]ACETAMIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OGA_BACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–716； UniProt 23–737 Author chain B； PDBConstruct 2–716； UniProt 23–737

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	2jiw
Deposition date deposition_date	2007-07-02
Structure title title	Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with 2- Acetylamino-2-deoxy-1-epivalienamine
Keywords keywords	O-GLCNACASE, GLYCOSIDASE, EPIVALIENAMINE, GH84, ENZYME, HYDROLASE, INHIBITOR, INHIBITION; HYDROLASE
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.

2jiw__assembly_1__model_1

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

Download this curve (.dat)

2jiw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2jiw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.99 Å
Rg (electron density)	27.40 Å
Total Rg	28.13 Å
Atom count	4813
Residues	590
Excluded volume	85492 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jiw__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2jiw__assembly_2__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	O-GLCNACASE BT_4395
Molecular weight formula_weight	82319.2 kDa
EC 编号 ec_number	3.2.1.52
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	10470

MNVSLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNVEQIKNLPLQVKANRVLISPANEVVKWAAGNSVEIELDAIYPGENIQINFGKDAPCTWGRLEISTDGKEWKTVDLKQKESRLSAGLQKAPVKFVRFTNVSDEEQQVYLRQFVLTIEKK

Source Source

Source organism organism	BACTEROIDES THETAIOTAOMICRON
NCBI taxonomy ID ncbi_taxonomy_id	226186
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	N-[(1S,2R,5R,6R)-2-AMINO-5,6-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOHEX-3-EN-1-YL]ACETAMIDE
Molecular weight formula_weight	216.2 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	766

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2jiwa1
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	d2jiwa2
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	d2jiwa3
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	d2jiwb1
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	d2jiwb2
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	d2jiwb3
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

CATH v4.4 (6 domains)

Domain ID domain_id	2jiwA01
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	2jiwA02
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	2jiwA03
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	2jiwB01
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	2jiwB02
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	2jiwB03
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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Unit-cell length a length_a	51.398 Å
Unit-cell length b length_b	94.131 Å
Unit-cell length c length_c	99.808 Å
Unit-cell angle α angle_alpha	104.97 °
Unit-cell angle β angle_beta	94.09 °
Unit-cell angle γ angle_gamma	102.48 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	95.350 Å
R factor r_factor	0.2080
R_work r_work	0.2060
R_free r_free	0.2480

Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with 2- Acetylamino-2-deoxy-1-epivalienamine

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

O-GLCNACASE BT_4395

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

2jiw__assembly_1__model_1

2jiw__assembly_1__model_1 | I(q)

2jiw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with 2- Acetylamino-2-deoxy-1-epivalienamine

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

O-GLCNACASE BT_4395

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

2jiw__assembly_1__model_1

2jiw__assembly_1__model_1 | I(q)

2jiw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)