SAXSdb — 8s72

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

Short neurotoxin 1

synthetic construct

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Heavy chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D. × 2 Light chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D. × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	3S11_NAJPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–64； UniProt 1–61 Author chain N； PDBConstruct 5–64； UniProt 1–61

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	8s72
Deposition date deposition_date	2024-02-28
Last revision last_revision	2025-09-10
Structure title title	Crystal structure of neutralizing Fab Eq4.Dp46-3D from equine antivenom bound to a consensus short chain three finger alpha-neurotoxin.
Keywords keywords	Monoclonal antibody, antivenom, complex, short chain alpha-neurotoxin, ANTITOXIN; ANTITOXIN
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.

8s72__assembly_1__model_1

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

Download this curve (.dat)

8s72__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8s72__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.24 Å
Rg (electron density)	43.96 Å
Total Rg	44.05 Å
Atom count	14268
Residues	997
Excluded volume	128640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8s72__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 (4)

Entity 1 Entity 1 polymer

Description description	Short neurotoxin 1
Molecular weight formula_weight	7117.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,A
Atom count atom_count	14484

GPGGMICYNQQSSQPPTTKTCSETSCYKKTWRDHRGTIIERGCGCPKVKPGIKLHCCRTDKCNN

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Heavy chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.
Molecular weight formula_weight	24573.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QVQLTESGPGLVKPSQTLSLTCTVSGLSLTNNVAGSGWVRQAPGKGLEWIGDISGDGVTYYNPALKPRVSITKDTSKSQVYLALNRLTGEDTAVYYCVGNADVYYWRDGEKYWGQGILVTVSSASTTAPKVFPLASHSAATSGSTVALGCLVSSYFPEPVTVSWNSGALTSGVHTFPSVLQSSGLYSLSSMVTVPASSLKSQTYICNVAHPASSTKVDKKIVIKECGLEVLFQ

Source Source

Source organism organism	Equus caballus
NCBI taxonomy ID ncbi_taxonomy_id	9796
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Light chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.
Molecular weight formula_weight	22803.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QSVTQPASVSGTLGQTVTISCSGSKSNIGDTPSYVGWFQQIPGTAPKTLIYGDGKRASGVPDRFSGSVSENTATLTISGVQAEDEADYWCASWDVNSDSEVFGGGTHLTVAGGPTSAPSVSLFPPSSEELSANKATVVCLISDFSPSGLEVIWKVNDAVTNDRVQTTRPSKQSNGKYAASSYLTRTSTEWKSYSSVSCQVKHQGKTVEKKLSPSECP

Source Source

Source organism organism	Equus caballus
NCBI taxonomy ID ncbi_taxonomy_id	9796
Host organism host_organism	Cricetulus griseus

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

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Unit-cell length a length_a	294.846 Å
Unit-cell length b length_b	294.846 Å
Unit-cell length c length_c	99.525 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	24

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	2.780 Å
Low-resolution limit resolution_low	20.600 Å
R factor r_factor	0.2283
R_work r_work	0.2276
R_free r_free	0.2495

Crystal structure of neutralizing Fab Eq4.Dp46-3D from equine antivenom bound to a consensus short chain three finger alpha-neurotoxin.

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

Short neurotoxin 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

8s72__assembly_1__model_1

8s72__assembly_1__model_1 | I(q)

8s72__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 water

7. Citations (1)

Crystal structure of neutralizing Fab Eq4.Dp46-3D from equine antivenom bound to a consensus short chain three finger alpha-neurotoxin.

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

Short neurotoxin 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

8s72__assembly_1__model_1

8s72__assembly_1__model_1 | I(q)

8s72__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 water

7. Citations (1)