3ee5

Crystal structure of human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in complex with GLCNAC-Beta1,3-Gal-Beta-Naphthalenemethanol

Method: X-RAY DIFFRACTION

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

Beta-1,4-galactosyltransferase 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose × 1 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE × 1 naphthalen-2-ylmethanol × 1 SULFATE ION × 5 MANGANESE (II) ION × 1 GLYCEROL × 2 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose × 1 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE × 1 naphthalen-2-ylmethanol × 1 SULFATE ION × 7 MANGANESE (II) ION × 1 GLYCEROL × 4 water × 1	Consistent with protein count
3	Other combination	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose × 1 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE × 1 naphthalen-2-ylmethanol × 1 SULFATE ION × 2 MANGANESE (II) ION × 1 GLYCEROL × 1 1,4-DIETHYLENE DIOXIDE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B4GT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–287； UniProt 126–398 Author chain B； PDBConstruct 15–287； UniProt 126–398 Author chain C； PDBConstruct 15–287； UniProt 126–398

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	3ee5
Deposition date deposition_date	2008-09-04
Structure title title	Crystal structure of human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in complex with GLCNAC-Beta1,3-Gal-Beta-Naphthalenemethanol
Keywords keywords	;Closed conformation, carbohydrate acceptor binding, Alternative initiation, Cell membrane, Congenital disorder of glycosylation, Glycoprotein, Glycosyltransferase, Golgi apparatus, Manganese, Membrane, Metal-binding, Secreted, Signal-anchor, Transferase, Transmembrane ;; TRANSFERASE
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.

3ee5__assembly_1__model_1

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

Download this curve (.dat)

3ee5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ee5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.00 Å
Rg (electron density)	17.80 Å
Total Rg	18.89 Å
Atom count	2325
Residues	273
Excluded volume	41147 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ee5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ee5__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ee5__assembly_3__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 (10)

Entity 1 Entity 1 polymer

Description description	Beta-1,4-galactosyltransferase 1
Molecular weight formula_weight	32773.2 kDa
EC 编号 ec_number	2.4.1.38
Mutation mutation	d126, M340H, C338T, R337T
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7469

ASMTGGQQMGRGSASLPACPEESPLLVGPMLIEFNMPVDLELVAKQNPNVKMGGRYAPRDCVSPHKVAIIIPFRNRQEHLKYWLYYLHPVLQRQQLDYGIYVINQAGDTIFNRAKLLNVGFQEALKDYDYTCFVFSDVDLIPMNDHNAYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLTINGFPNNYWGWGGEDDDIFNRLVFRGMSISRPNAVVGTTRHIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYQVLDVQRYPLYTQITVDIGTPS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose
Molecular weight formula_weight	383.3 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
Molecular weight formula_weight	503.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	naphthalen-2-ylmethanol
Molecular weight formula_weight	158.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 6 Entity 6 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 8 Entity 8 non-polymer

Description description	1,4-DIETHYLENE DIOXIDE
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	475

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3ee5a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.2 — beta 1,4 galactosyltransferase (b4GalT1)

Domain ID domain_id	d3ee5b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.2 — beta 1,4 galactosyltransferase (b4GalT1)

Domain ID domain_id	d3ee5c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.2 — beta 1,4 galactosyltransferase (b4GalT1)

CATH v4.4 (3 domains)

Domain ID domain_id	3ee5A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	3ee5B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	3ee5C00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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Unit-cell length a length_a	107.127 Å
Unit-cell length b length_b	195.742 Å
Unit-cell length c length_c	143.801 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	24

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	46.330 Å
R factor r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2400

Crystal structure of human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in complex with GLCNAC-Beta1,3-Gal-Beta-Naphthalenemethanol

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

Beta-1,4-galactosyltransferase 1

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

3ee5__assembly_1__model_1

3ee5__assembly_1__model_1 | I(q)

3ee5__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in complex with GLCNAC-Beta1,3-Gal-Beta-Naphthalenemethanol

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

Beta-1,4-galactosyltransferase 1

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

3ee5__assembly_1__model_1

3ee5__assembly_1__model_1 | I(q)

3ee5__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)