SAXSdb — 5ky5

▼

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

GDP-fucose protein O-fucosyltransferase 1

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	EGF(+) × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GUANOSINE-5'-DIPHOSPHATE × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OFUT1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–355； UniProt 33–384

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ky5
Deposition date deposition_date	2016-07-21
Structure title title	mouse POFUT1 in complex with EGF(+) and GDP
Keywords keywords	glycosyltransferase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5ky5__assembly_1__model_1

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

Download this curve (.dat)

5ky5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ky5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.27 Å
Rg (electron density)	21.50 Å
Total Rg	22.42 Å
Atom count	6188
Residues	392
Excluded volume	56092 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ky5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	GDP-fucose protein O-fucosyltransferase 1
Molecular weight formula_weight	40457.3 kDa
EC 编号 ec_number	2.4.1.221
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	6699

GAPSWDLAGYLLYCPCMGRFGNQADHFLGSLAFAKLLNRTLAVPPWIEYQHHKPPFTNLHVSYQKYFKLEPLQAYHRVVSLEDFMENLAPSHWPPEKRVAYCFEVAAQRSPDKKTCPMKEGNPFGPFWDQFHVSFNKSELFTGISFSASYKEQWTQRFPAKEHPVLALPGAPAQFPVLEEHRELQKYMVWSDEMVRTGEALISAHLVRPYVGIHLRIGSDWKNACAMLKDGTAGSHFMASPQCVGYSRSTATPLTMTMCLPDLKEIQRAVTLWVRALNARSVYIATDSESYVSEIQQLFKDKVRVVSLKPEVAQIDLYILGQADHFIGNCVSSFTAFVKRERDLHGRQSSFFGMD

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	EGF(+)
Molecular weight formula_weight	4111.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DIDECASNPCQNGGTCVNTVGSYTCLCPPGFTGPNCEDDI

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
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	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	448

▼

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5ky5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11340 —

Domain ID domain_id	5ky5A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11350 —

Domain ID domain_id	5ky5B00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

▶

Unit-cell length a length_a	52.080 Å
Unit-cell length b length_b	67.030 Å
Unit-cell length c length_c	111.100 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	47.156 Å
R factor r_factor	0.1583
R_work r_work	0.1575
R_free r_free	0.1728

mouse POFUT1 in complex with EGF(+) and GDP

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

GDP-fucose protein O-fucosyltransferase 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

5ky5__assembly_1__model_1

5ky5__assembly_1__model_1 | I(q)

5ky5__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 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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

mouse POFUT1 in complex with EGF(+) and GDP

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

GDP-fucose protein O-fucosyltransferase 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

5ky5__assembly_1__model_1

5ky5__assembly_1__model_1 | I(q)

5ky5__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 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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)