SAXSdb — 4ydv

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

HIV ANTIBODY 7B2 LIGHT CHAIN,Ig kappa chain C region

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	HIV GP41 PEPTIDE GP41(596-606) × 1 HIV ANTIBODY 7B2 HEAVY CHAIN,IgG H chain × 1 （S6B291） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	HIV GP41 PEPTIDE GP41(596-606) × 1 HIV ANTIBODY 7B2 HEAVY CHAIN,IgG H chain × 1 （S6B291） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGKC_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 160–265； UniProt 1–106 Author chain L； PDBConstruct 160–265； UniProt 1–106

HIV ANTIBODY 7B2 HEAVY CHAIN,IgG H chain

Homo sapiens

UniProt S6B291

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	HIV GP41 PEPTIDE GP41(596-606) × 1 HIV ANTIBODY 7B2 LIGHT CHAIN,Ig kappa chain C region × 1 （P01834） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	HIV GP41 PEPTIDE GP41(596-606) × 1 HIV ANTIBODY 7B2 LIGHT CHAIN,Ig kappa chain C region × 1 （P01834） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S6B291_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 143–252； UniProt 132–241 Author chain H； PDBConstruct 143–252； UniProt 132–241

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	4ydv
Deposition date deposition_date	2015-02-23
Structure title title	STRUCTURE OF THE ANTIBODY 7B2 THAT CAPTURES HIV-1 VIRIONS
Keywords keywords	IGG, HIV, ANTIBODY, HIV GP41 ENVELOPE PROTEIN, 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.

4ydv__assembly_1__model_1

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

Download this curve (.dat)

4ydv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ydv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.59 Å
Rg (electron density)	24.75 Å
Total Rg	25.61 Å
Atom count	3357
Residues	437
Excluded volume	59376 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ydv__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ydv__assembly_2__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	HIV GP41 PEPTIDE GP41(596-606)
Molecular weight formula_weight	1193.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q
Atom count atom_count	6805

XWGCSGKLICTTX

Entity 2 Entity 2 polymer

Description description	HIV ANTIBODY 7B2 LIGHT CHAIN,Ig kappa chain C region
Molecular weight formula_weight	29180.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,A

METDTLLLWVLLLWVPGSTGDDIQMTQSPASLAVPLLLWISGAYGDIVLAQSPDSLAVSPGERATIHCKSSQTLLYSSNNRHSIAWYQQRPGQPPKLLLYWASMRLSGVPDRFSGSGSGTDFTLTINNLQAEDVAIYYCHQYSSHPPTFGHGTRVELRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	HOMO SAPIENS

Entity 3 Entity 3 polymer

Description description	HIV ANTIBODY 7B2 HEAVY CHAIN,IgG H chain
Molecular weight formula_weight	27207.6 kDa
Mutation mutation	YES,YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,B

METDTLLLWVLLLWVPGSTGDQVQLVQSGGGVFKPGGSLRLSCEASGFTFTEYYMTWVRQAPGKGLEWLAYISKNGEYSKYSPSSNGRFTISRDNAKNSVFLQLDRLSADDTAVYYCARADGLTYFSELLQYIFDLWGQGARVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	HOMO SAPIENS

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4ydvA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ydvA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ydvB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ydvB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ydvH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ydvH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ydvL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ydvL02
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	73.434 Å
Unit-cell length b length_b	76.281 Å
Unit-cell length c length_c	127.627 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.800 Å
R factor r_factor	0.1910
R_work r_work	0.1890
R_free r_free	0.2230

STRUCTURE OF THE ANTIBODY 7B2 THAT CAPTURES HIV-1 VIRIONS

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

HIV ANTIBODY 7B2 LIGHT CHAIN,Ig kappa chain C region

State in the Current Structure

Other States of the Same Protein in the Database

HIV ANTIBODY 7B2 HEAVY CHAIN,IgG H 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

4ydv__assembly_1__model_1

4ydv__assembly_1__model_1 | I(q)

4ydv__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

STRUCTURE OF THE ANTIBODY 7B2 THAT CAPTURES HIV-1 VIRIONS

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

HIV ANTIBODY 7B2 LIGHT CHAIN,Ig kappa chain C region

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HIV ANTIBODY 7B2 HEAVY CHAIN,IgG H 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

4ydv__assembly_1__model_1

4ydv__assembly_1__model_1 | I(q)

4ydv__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)