SAXSdb — 2vca

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

ALPHA-N-ACETYLGLUCOSAMINIDASE

CLOSTRIDIUM PERFRINGENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GLYCEROL × 3 SULFATE ION × 1 CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q0TST1_CLOP1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–891； UniProt 26–916

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	2vca
Deposition date deposition_date	2007-09-19
Structure title title	Family 89 glycoside hydrolase from Clostridium perfringens in complex with beta-N-acetyl-D-glucosamine
Keywords keywords	;MUCOPOLYSACCHARIDOSIS, BETA-N-ACETYL-D-GLUCOSAMINE, GH89, NAGLU, SANFILIPPO DISEASE, HYDROLASE, ALPHA-N-ACETYLGLUCOSAMINIDASE, FAMILY 89 GLYCOSIDE HYDROLASE ;; 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.

2vca__assembly_1__model_1

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

Download this curve (.dat)

2vca__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vca__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.76 Å
Rg (electron density)	28.63 Å
Total Rg	29.48 Å
Atom count	7215
Residues	887
Excluded volume	126970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vca__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	ALPHA-N-ACETYLGLUCOSAMINIDASE
Molecular weight formula_weight	102273.2 kDa
EC 编号 ec_number	3.2.1.50
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	8132

GVEITEGVTVTAKGNTEGNTADLAIDGDLSTYWESSNDYKWIEVDLGGIYELSKIEIFNKDEAVYKYNIYASEDGENFNKIAYKNNDNVSDSNGNMHTIDNVRAGKIRIDVVQNSNSDRVNIAEINVFGKNTGESLPEVKKIATSNFSETPWATEYEKFNSDSAYANEKTLNEIKNLVGRVIGREFKDKFIFEIRDQLNGNDVFEVSDSGDGKVLIKGNNGVSLASGFNYYLKNYCNVSYNPIMGSNLKMPETMPSVGERVVIDTPYEHRYALNFCTYSYTMSFWDWDQYEEFLDWCAMNGVNLVLDIIGQEEVLRRTLNEFGYSDEEVKEFISGPAYFAWFYMQNMTGFGGPLPNDWFEQRAELGRKMHDRMQSFGINPVLQGYSGMVPRDFKEKNQEAQTISQGGWCGFDRPDMLKTYVNEGEADYFQKVADVFYEKQKEVFGDVTNFYGVDPFHEGGNTGDLDNGKIYEIIQNKMIEHDNDAVWVIQNWQGNPSNNKLEGLTKKDQAMVLDLFSEVSPDWNRLEERDLPWIWNMLHNFGGRMGMDAAPEKLATEIPKALANSEHMVGIGITPEAINTNPLAYELLFDMAWTRDQINFRTWTEDYIERRYGKTNKEILEAWNIILDTAYKKRNDYYQGAAESIINARPGFGIKSASTWGHSKIVYDKSEFEKAIEIFAKNYDEFKDSDAFLYDFADILKQLLANSAQEYYEVMCNAYNNGNGEKFKFVSGKFLELIKLQERVLSTRPEFLIGNWIEDARTMLKDSDDWTKDLFEFNARALVTTWGSRNNADGGGLKDYSNRQWSGLTEDYYYARWEKWINGLQAELDGGAKAPNIDWFKMEYDWVNKKSDTDKLYPTEASNENLGELAKIAMESYSVTNMDKILGENES

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	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 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	887

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2vcaA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2vcaA02
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	2vcaA03
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	2vcaA04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	670 — N-acetyl-b-d-glucoasminidase

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Unit-cell length a length_a	90.773 Å
Unit-cell length b length_b	90.773 Å
Unit-cell length c length_c	252.779 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	2.050 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1920
R_work r_work	0.1900
R_free r_free	0.2300

Family 89 glycoside hydrolase from Clostridium perfringens in complex with beta-N-acetyl-D-glucosamine

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

ALPHA-N-ACETYLGLUCOSAMINIDASE

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

2vca__assembly_1__model_1

2vca__assembly_1__model_1 | I(q)

2vca__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Family 89 glycoside hydrolase from Clostridium perfringens in complex with beta-N-acetyl-D-glucosamine

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

ALPHA-N-ACETYLGLUCOSAMINIDASE

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

2vca__assembly_1__model_1

2vca__assembly_1__model_1 | I(q)

2vca__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)