2fyd

catalytic domain of bovine beta 1, 4-galactosyltransferase in complex with alpha-lactalbumin, glucose, Mn, and UDP-N-acetylgalactosamine

Method: X-RAY DIFFRACTION

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

Alpha-lactalbumin

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	beta-1,4-galactosyltransferase × 1 CALCIUM ION × 1 TETRAETHYLENE GLYCOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-galactopyranose × 1 MANGANESE (II) ION × 1 URIDINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	beta-1,4-galactosyltransferase × 1 CALCIUM ION × 1 TETRAETHYLENE GLYCOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-galactopyranose × 1 MANGANESE (II) ION × 1 URIDINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LALBA_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 21–143 Author chain C； PDBConstruct 1–123； UniProt 21–143

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	2fyd
Deposition date deposition_date	2006-02-07
Structure title title	catalytic domain of bovine beta 1, 4-galactosyltransferase in complex with alpha-lactalbumin, glucose, Mn, and UDP-N-acetylgalactosamine
Keywords keywords	lactose sythase, catalytic intermediate, TRANSFERASE; 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.

2fyd__assembly_1__model_1

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

Download this curve (.dat)

2fyd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fyd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.93 Å
Rg (electron density)	22.26 Å
Total Rg	23.19 Å
Atom count	3268
Residues	395
Excluded volume	58242 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fyd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2fyd__assembly_2__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 (10)

Entity 1 Entity 1 polymer

Description description	Alpha-lactalbumin
Molecular weight formula_weight	14015.8 kDa
Mutation mutation	W312C, C342T, P401C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7045

TELTKCKVSHAIKDIDGYQGISLLEWACVLFHTSGYDTQAVVNDNGSTEYGLFQISDRFWCKSSEFPESENICGISCDKLLDDELDDDIACAKKILAIKGIDYWKAYKPMCSEKLEQWRCEKP

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	beta-1,4-galactosyltransferase
Molecular weight formula_weight	32772.5 kDa
EC 编号 ec_number	2.4.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

ASMTGGQQMGRGSSLTACPEESPLLVGPMLIEFNIPVDLKLVEQQNPKVKLGGRYTPMDCISPHKVAIIIPFRNRQEHLKYWLYYLHPILQRQQLDYGIYVINQAGESMFNRAKLLNVGFKEALKDYDYNCFVFSDVDLIPMNDHNTYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLSINGFPNNYCGWGGEDDDIYNRLAFRGMSVSRPNAVIGKTRMIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYMVLEVQRYPLYTKITVDIGTCS

Source Source

Source organism organism	Bos taurus
Common name common_name	cattle
NCBI taxonomy ID ncbi_taxonomy_id	9913
Host organism host_organism	Escherichia coli BL21

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	2

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 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	2

Entity 6 Entity 6 non-polymer

Description description	beta-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-galactopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	509

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2fyda_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.2 — Lysozyme-like
Superfamily Superfamily superfamily	d.2.1 — Lysozyme-like
Family Family family	d.2.1.2 — C-type lysozyme

Domain ID domain_id	d2fydb1
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	d2fydc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.2 — Lysozyme-like
Superfamily Superfamily superfamily	d.2.1 — Lysozyme-like
Family Family family	d.2.1.2 — C-type lysozyme

Domain ID domain_id	d2fydd_
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 (4 domains)

Domain ID domain_id	2fydA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2fydB00
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	2fydC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2fydD00
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	58.068 Å
Unit-cell length b length_b	95.376 Å
Unit-cell length c length_c	100.389 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	32.080 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2420

catalytic domain of bovine beta 1, 4-galactosyltransferase in complex with alpha-lactalbumin, glucose, Mn, and UDP-N-acetylgalactosamine

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

Alpha-lactalbumin

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

2fyd__assembly_1__model_1

2fyd__assembly_1__model_1 | I(q)

2fyd__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 polymer

Polymer Polymer

Source Source

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

catalytic domain of bovine beta 1, 4-galactosyltransferase in complex with alpha-lactalbumin, glucose, Mn, and UDP-N-acetylgalactosamine

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

Alpha-lactalbumin

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

2fyd__assembly_1__model_1

2fyd__assembly_1__model_1 | I(q)

2fyd__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 polymer

Polymer Polymer

Source Source

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)