3gwj

Crystal structure of Antheraea pernyi arylphorin

Method: X-RAY DIFFRACTION

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

Arylphorin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 6 其他Polymer 12	;alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 FORMIC ACID × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARY_ANTPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–674； UniProt 24–697 Author chain B； PDBConstruct 1–674； UniProt 24–697 Author chain C； PDBConstruct 1–674； UniProt 24–697 Author chain D； PDBConstruct 1–674； UniProt 24–697 Author chain E； PDBConstruct 1–674； UniProt 24–697 Author chain F； PDBConstruct 1–674； UniProt 24–697

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	3gwj
Deposition date deposition_date	2009-04-01
Structure title title	Crystal structure of Antheraea pernyi arylphorin
Keywords keywords	Arylphorin, Mono-glucosylated N-glycan, stability, glycosylation, Glycoprotein, Secreted, Storage protein, OXYGEN TRANSPORT; OXYGEN TRANSPORT
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.

3gwj__assembly_1__model_1

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

Download this curve (.dat)

3gwj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gwj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.06 Å
Rg (electron density)	46.24 Å
Total Rg	46.86 Å
Atom count	35322
Residues	4044
Excluded volume	629270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gwj__assembly_1__model_1`	hexameric （6）	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	Arylphorin
Molecular weight formula_weight	80502.4 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	36702

HVLKTKDVDTVFVERQKKVLSLFQDVDQLNTNDEYYKIGKDYDIEANIDNYTNKKAVEDFLKMYRCGFLPKYNEFSVFHDKLRDEAIALFHLFYYAKDFDTFYKSAAFARVHLNQGQFLYAYYIAIIQRKDTYGIVLPAPYEIYPELFVNIDTTYKMFRTKMQNGLINPEAAVEYGIVKEDNHYVYYSNYSNAITYYNEEQRLAYFTEDIGLNAYYFFFHIHLPFWWTAEKYGNLKERRGEMYHYFYDQLLTRYYFERLTNGLGTIPEFSWYSPVKTGHYPLLTSYYTPFSQRPNFYNVHSEENYEKIRFLDAYENYFVQALQKGVFEGFGQTIYLNDSKANSFVGNYWQDNADLYGEEVTKDYQRSYEIVARQVLGAAPKPFDKYTFMPSALDFYQTSLRDPTFYQLYNRIIGYFNQFKQYLEPHSQEKLHFVGVKVNNVVVDKLVTFFEYYDFDATNTVFLTEEELKTKYPHNLKVRQPRLNHQPFNINIDIKADVATDAVVKIFMGPKYNENGFPITLENDWMKFFEMDWFTHKITPGQNTIVRNSNEFVIFKEDSLPSTELYKLLEKGKVPFDMSEDFGYLPKRLMLPRGTKGGFPFQFVVFVYPFESTTKNLTPYEKFMIDNKPLGYPFDRPVDTSCFKQPNIFFRDVSVYHEGEYHAYEYNVPAYFSH

Entity 2 Entity 2 branched

Description description	;alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	2045.8 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1380

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3gwjA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	3gwjA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

Domain ID domain_id	3gwjB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	3gwjB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

Domain ID domain_id	3gwjC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	3gwjC03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

Domain ID domain_id	3gwjD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	3gwjD03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

Domain ID domain_id	3gwjE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	3gwjE03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

Domain ID domain_id	3gwjF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	3gwjF03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

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Unit-cell length a length_a	121.196 Å
Unit-cell length b length_b	119.470 Å
Unit-cell length c length_c	319.878 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.430 Å
Low-resolution limit resolution_low	48.800 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2290

Crystal structure of Antheraea pernyi arylphorin

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

Arylphorin

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

3gwj__assembly_1__model_1

3gwj__assembly_1__model_1 | I(q)

3gwj__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

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of Antheraea pernyi arylphorin

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

Arylphorin

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

3gwj__assembly_1__model_1

3gwj__assembly_1__model_1 | I(q)

3gwj__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

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)