3igu

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

Method: X-RAY DIFFRACTION

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

Alpha-N-acetylgalactosaminidase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 4	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GLYCEROL × 15 2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAGAB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–394； UniProt 18–411 Author chain B； PDBConstruct 1–394； UniProt 18–411

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	3igu
Deposition date deposition_date	2009-07-28
Structure title title	Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate
Keywords keywords	;GLYCOPROTEIN, CARBOHYDRATE-BINDING PROTEIN, GLYCOSIDASE, LYSOSOMAL ENZYME, (BETA/ALPHA)8 BARREL, Schindler disease, Kanzaki disease, Disease mutation, Disulfide bond, Epilepsy, Hydrolase, Lysosome, Phosphoprotein ;; 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.

3igu__assembly_1__model_1

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

Download this curve (.dat)

3igu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3igu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.47 Å
Rg (electron density)	29.71 Å
Total Rg	30.43 Å
Atom count	6492
Residues	774
Excluded volume	115720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3igu__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Description description	Alpha-N-acetylgalactosaminidase
Molecular weight formula_weight	45582.9 kDa
EC 编号 ec_number	3.2.1.49
Mutation mutation	N201Q
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	7197

LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	TRICHOPLUSIA NI

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 6 Entity 6 non-polymer

Description description	2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose
Molecular weight formula_weight	200.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 7 Entity 7 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	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	675

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3igua1
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.1.8.1 — Amylase, catalytic domain

Domain ID domain_id	d3igua2
Class class	b — All beta proteins
Fold Fold fold	b.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
Family Family family	b.71.1.0 — automated matches

Domain ID domain_id	d3igub1
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.1.8.1 — Amylase, catalytic domain

Domain ID domain_id	d3igub2
Class class	b — All beta proteins
Fold Fold fold	b.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
Family Family family	b.71.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3iguA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3iguA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	3iguB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3iguB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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Unit-cell length a length_a	151.612 Å
Unit-cell length b length_b	113.649 Å
Unit-cell length c length_c	68.415 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.14 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	45.980 Å
R factor r_factor	0.1660
R_work r_work	0.1640
R_free r_free	0.1990

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

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

Alpha-N-acetylgalactosaminidase

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

3igu__assembly_1__model_1

3igu__assembly_1__model_1 | I(q)

3igu__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

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

Alpha-N-acetylgalactosaminidase

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

3igu__assembly_1__model_1

3igu__assembly_1__model_1 | I(q)

3igu__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)