2zuu

Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc

Method: X-RAY DIFFRACTION

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

Lacto-N-biose phosphorylase

Bifidobacterium longum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-acetamido-2-deoxy-alpha-D-glucopyranose × 2 GLYCEROL × 2 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2-acetamido-2-deoxy-alpha-D-glucopyranose × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5NU17_BIFLO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–751； UniProt 1–751 Author chain B； PDBConstruct 1–751； UniProt 1–751 Author chain C； PDBConstruct 1–751； UniProt 1–751 Author chain D； PDBConstruct 1–751； UniProt 1–751

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	2zuu
Deposition date deposition_date	2008-10-28
Structure title title	Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc
Keywords keywords	beta-alpha-barrel, TIM barrel, Glycosyltransferase, 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.

2zuu__assembly_1__model_1

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

Download this curve (.dat)

2zuu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zuu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.14 Å
Rg (electron density)	36.57 Å
Total Rg	36.97 Å
Atom count	11790
Residues	1477
Excluded volume	207620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zuu__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zuu__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 (5)

Entity 1 Entity 1 polymer

Description description	Lacto-N-biose phosphorylase
Molecular weight formula_weight	85484.1 kDa
EC 编号 ec_number	2.4.1.211
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	25272

MTSTGRFTLPSEENFAEKTKELAELWGADAIRNSDGTHLDEAVLALGKKIYNAYFPTRAHNEWITLHMDETPQVYLLTDRILAESDTVDIPLMESFFAEQLKPNRDADPHKYWEVVDRTTGEVVDSANWTLDADEDTVHVSGVAAWHEYTVSFLAYIIWDPVEMYNHLTNDWGDKEHEIPFDIYHPATRKFVFDTFEQWLKDSPQTDVVRFTTFFYQFTLLFDEKRREKVVDWFGCACTVSPRALDDFEAKYGYRLRPEDFVDGGAYNSAWRVPRKAQRDWIDFLSGFVRENVKQLADMSHAAGKEAMMFLGDQWIGTEPYKDGFDELGLDAVVGSIGDGTTTRMIADIPGVKYTEGRFLPYFFPDTFYEGNDPSIEGLDNWRKARRAILRSPISRMGYGGYLSLAAKFPKFVDTVTHIANEFRDIHDRTGGVAAEGELNVAILNSWGKMRSWMAFTVAHALPNKQTYSYYGILESLSGMRVNVRFISFDDVLAHGIDSDIDVIINGGPVDTAFTGGDVWTNPKLVETVRAWVRGGGAFVGVGEPSSAPRFQTGRFFQLADVIGVDEERYQTLSVDKYFPPVVPDHFITADVPVDPAAREAWEQAGYRIPLSGCGGGQSIKPLGGIDFGEPVLNTYPVNENVTLLRADGGQVQLATNDYGKGRGVYISGLPYSAANARLLERVLFYASHNEDKYAAWSSSNPECEVAHFPEQGLYCVINNTDQPQKTTVTLADGTTEDFDLPDSGIAWREALEHHHHHH

Source Source

Source organism organism	Bifidobacterium longum
NCBI taxonomy ID ncbi_taxonomy_id	216816
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-alpha-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	4

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	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1638

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	2zuuA01
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	2zuuA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zuuA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

Domain ID domain_id	2zuuA04
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	2zuuB01
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	2zuuB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zuuB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

Domain ID domain_id	2zuuB04
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	2zuuC01
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	2zuuC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zuuC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

Domain ID domain_id	2zuuC04
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	2zuuD01
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	2zuuD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zuuD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

Domain ID domain_id	2zuuD04
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	67.777 Å
Unit-cell length b length_b	111.484 Å
Unit-cell length c length_c	118.432 Å
Unit-cell angle α angle_alpha	105.19 °
Unit-cell angle β angle_beta	90.48 °
Unit-cell angle γ angle_gamma	107.35 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	40.680 Å
R factor r_factor	0.1730
R_work r_work	0.1700
R_free r_free	0.2310

Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc

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

Lacto-N-biose phosphorylase

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

2zuu__assembly_1__model_1

2zuu__assembly_1__model_1 | I(q)

2zuu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (2)

Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc

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

Lacto-N-biose phosphorylase

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

2zuu__assembly_1__model_1

2zuu__assembly_1__model_1 | I(q)

2zuu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (2)