SAXSdb — 6bkd

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

Polyprotein

Recombinant Hepatitis C virus HK6a/JFH-1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Fab AR3D heavy chain × 1 （S6B2A6） Fab AR3D light chain × 1 （Q6PIL8） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B9V0E2_9HEPC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–48； UniProt 412–459 Author chain E； PDBConstruct 53–135； UniProt 488–570 Author chain E； PDBConstruct 142–189； UniProt 604–651

Fab AR3D heavy chain

Homo sapiens

UniProt S6B2A6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Polyprotein × 1 （B9V0E2） Fab AR3D light chain × 1 （Q6PIL8） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S6B2A6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 119–232； UniProt 134–247

Fab AR3D light chain

Homo sapiens

UniProt Q6PIL8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Polyprotein × 1 （B9V0E2） Fab AR3D heavy chain × 1 （S6B2A6） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6PIL8_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain L； PDBConstruct 95–212； UniProt 119–236

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	6bkd
Deposition date deposition_date	2017-11-08
Structure title title	Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3D
Keywords keywords	hepatitis C virus, HCV, broadly neutralizing antibodies, bNAbs, E2 core, IGHV1-69, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

6bkd__assembly_1__model_1

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

Download this curve (.dat)

6bkd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6bkd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.54 Å
Rg (electron density)	32.93 Å
Total Rg	33.27 Å
Atom count	4440
Residues	580
Excluded volume	78683 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6bkd__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Polyprotein
Molecular weight formula_weight	20707.4 kDa
Mutation mutation	N448D
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	4440

QLINTNGSWHINRTALNCNDSLQTGFITSLFYAKNVDSSGCPERMAACGSSGCWHYAPRPCDVVSARTVCGPVYCFTPSPVVVGTTDKLGIPTYNWGENETDVFMLESLRPPTGGWFGCTWMNSTGFTKTCGAPPGGPTDGGSGPWITPRCLVDYPYRLWHYPCTVNFTLHKVRMFVGGIEHRFDAACN

Source Source

Source organism organism	Recombinant Hepatitis C virus HK6a/JFH-1
NCBI taxonomy ID ncbi_taxonomy_id	595609
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Fab AR3D heavy chain
Molecular weight formula_weight	24458.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

LLEQSGAEVKKPGSSVKVSCKASGDTFRSYVITWARQAPGQGLEWMGAIIPFFGTTNLAQKFQGRVTITADESTKTVYMDLSSLRSDDTAVYYCAKAGDLSVGGVLAGGVPHLRHFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Fab AR3D light chain
Molecular weight formula_weight	23047.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ELTQSPGTLSLSPGERATLSCRAGQTVASNSLAWYQHKPGQAPRLLIYGASIRASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGLSSTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 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	1

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6bkdH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6bkdL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6bkdL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	37.318 Å
Unit-cell length b length_b	60.392 Å
Unit-cell length c length_c	148.082 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	88.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	49.330 Å
R factor r_factor	0.2698
R_work r_work	0.2679
R_free r_free	0.2861

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3D

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

Polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Fab AR3D heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Fab AR3D light chain

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

6bkd__assembly_1__model_1

6bkd__assembly_1__model_1 | I(q)

6bkd__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3D

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

Polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fab AR3D heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fab AR3D light chain

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

6bkd__assembly_1__model_1

6bkd__assembly_1__model_1 | I(q)

6bkd__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)