SAXSdb — 8ay1

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

GDP-fucose protein O-fucosyltransferase 2,Spondin-1

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1,2-ETHANEDIOL × 11 SULFATE ION × 12 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3B7D6_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 409–462； UniProt 613–666 Author chain B； PDBConstruct 409–462； UniProt 613–666

GDP-fucose protein O-fucosyltransferase 2,Spondin-1

Caenorhabditis elegans

UniProt Q8WR51

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1,2-ETHANEDIOL × 11 SULFATE ION × 12 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OFUT2_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–386； UniProt 39–424 Author chain B； PDBConstruct 1–386； UniProt 39–424

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	8ay1
Deposition date deposition_date	2022-09-01
Structure title title	Crystal structure of the C. elegans POFUT2 (CePoFUT2) triple mutant (R298K-R299K-A418C) in complex with the Rattus norvegicus TSR4 single mutant (E10C) from F-spondin
Keywords keywords	PoFUT2, TSR, water molecules, Protein O-fucosylation, 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.

8ay1__assembly_1__model_1

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

Download this curve (.dat)

8ay1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ay1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.36 Å
Rg (electron density)	29.67 Å
Total Rg	30.44 Å
Atom count	7064
Residues	830
Excluded volume	125060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ay1__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 (6)

Entity 1 Entity 1 polymer

Description description	GDP-fucose protein O-fucosyltransferase 2,Spondin-1
Molecular weight formula_weight	53320.2 kDa
EC 编号 ec_number	2.4.1.221
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	7237

AEKKFLLYDVNFGEGFNLRRDVYMRVANTVRSLRDSGENYILVLPPWGRLHHWKRMEVALSWRLFFDLESLNRFIPVIEFEDFLDENRPIDQVIYLQHYAEGWGTEYVRKFEKRSCLPPAESHYKQVEEFKWKGWFYSYEDVYSRNFQCVSIQGDSGTLKDLLKHSNFSESTSIMVDRAETILHEHYGEVDYWKARRSMRYSNDLVDVADAFRKKYLDSDDKRDKTKLVDDWTKEKPRRTAIGGPYLGIHWRRRDFLYAKKAQLPTIPGTAKILQDLCKKLDLQKIYLATDAPDQEVDELKALLNGELEVYRFTDTQKLNDGQIAIIDQYLCAHAAYFIGSYESTFTFRIQEDREIIGFPISTTFNRLCPDTEPTCEQPCKWKIVYSSGGGGSGGGGSGGGGGSSGSSIPCLLSPWSCWSDCSVTCGKGMRTRQRMLKSLAELGDCNEDLEQAEKCMLPECP

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

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	155

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	8ay1A01
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	8ay1A02
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	8ay1B01
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	8ay1B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11350 —

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Unit-cell length a length_a	156.848 Å
Unit-cell length b length_b	156.848 Å
Unit-cell length c length_c	80.451 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	19.900 Å
R factor r_factor	0.1953
R_work r_work	0.1935
R_free r_free	0.2404

Crystal structure of the C. elegans POFUT2 (CePoFUT2) triple mutant (R298K-R299K-A418C) in complex with the Rattus norvegicus TSR4 single mutant (E10C) from F-spondin

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

GDP-fucose protein O-fucosyltransferase 2,Spondin-1

State in the Current Structure

Other States of the Same Protein in the Database

GDP-fucose protein O-fucosyltransferase 2,Spondin-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

8ay1__assembly_1__model_1

8ay1__assembly_1__model_1 | I(q)

8ay1__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 non-polymer

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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the C. elegans POFUT2 (CePoFUT2) triple mutant (R298K-R299K-A418C) in complex with the Rattus norvegicus TSR4 single mutant (E10C) from F-spondin

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

GDP-fucose protein O-fucosyltransferase 2,Spondin-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

GDP-fucose protein O-fucosyltransferase 2,Spondin-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

8ay1__assembly_1__model_1

8ay1__assembly_1__model_1 | I(q)

8ay1__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 non-polymer

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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)