6v06

Crystal structure of Beta-2 glycoprotein I purified from plasma (pB2GPI)

Method: X-RAY DIFFRACTION

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

Beta-2-glycoprotein 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 4	;alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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 ; × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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 ; × 1 ;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-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 ; × 1 SULFATE ION × 13 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APOH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–326； UniProt 20–345

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	6v06
Deposition date deposition_date	2019-11-18
Structure title title	Crystal structure of Beta-2 glycoprotein I purified from plasma (pB2GPI)
Keywords keywords	PLASMA GLYCOPROTEIN, COAGULATION, INNATE IMMUNE SYSTEM, AUTOIMMUNITY, THROMBOSIS, SUSHI DOMAIN, BLOOD CLOTTING; BLOOD CLOTTING
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.

6v06__assembly_1__model_1

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

Download this curve (.dat)

6v06__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6v06__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.78 Å
Rg (electron density)	45.22 Å
Total Rg	44.88 Å
Atom count	2945
Residues	326
Excluded volume	52251 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6v06__assembly_1__model_1`	monomeric （1）	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 (8)

Entity 1 Entity 1 polymer

Description description	Beta-2-glycoprotein 1
Molecular weight formula_weight	36299.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3374

GRTCPKPDDLPFSTVVPLKTFYEPGEEITYSCKPGYVSRGGMRKFICPLTGLWPINTLKCTPRVCPFAGILENGAVRYTTFEYPNTISFSCNTGFYLNGADSAKCTEEGKWSPELPVCAPIICPPPSIPTFATLRVYKPSAGNNSLYRDTAVFECLPQHAMFGNDTITCTTHGNWTKLPECREVKCPFPSRPDNGFVNYPAKPTLYYKDKATFGCHDGYSLDGPEEIECTKLGNWSAMPSCKASCKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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	1479.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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	1479.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-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	951.9 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	man
Copy count entity_count	13

Entity 7 Entity 7 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	429

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d6v06a1
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

Domain ID domain_id	d6v06a2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

Domain ID domain_id	d6v06a3
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

Domain ID domain_id	d6v06a4
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

Domain ID domain_id	d6v06a5
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	6v06A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

Domain ID domain_id	6v06A02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

Domain ID domain_id	6v06A03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

Domain ID domain_id	6v06A04
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

Domain ID domain_id	6v06A05
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

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Unit-cell length a length_a	160.843 Å
Unit-cell length b length_b	166.943 Å
Unit-cell length c length_c	114.049 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	36.600 Å
R factor r_factor	0.2020
R_work r_work	0.2010
R_free r_free	0.2360

Crystal structure of Beta-2 glycoprotein I purified from plasma (pB2GPI)

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

Beta-2-glycoprotein 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

6v06__assembly_1__model_1

6v06__assembly_1__model_1 | I(q)

6v06__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (2)

Crystal structure of Beta-2 glycoprotein I purified from plasma (pB2GPI)

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

Beta-2-glycoprotein 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

6v06__assembly_1__model_1

6v06__assembly_1__model_1 | I(q)

6v06__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (2)