SAXSdb — 9riu

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

Short neurotoxin 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Variable Domain of Heavy-Chain only Antibody (VHH) × 1 NICKEL (II) ION × 9 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Variable Domain of Heavy-Chain only Antibody (VHH) × 1 NICKEL (II) ION × 7 water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–61； UniProt 1–61 Author chain D； PDBConstruct 1–61； 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	9riu
Deposition date deposition_date	2025-06-11
Structure title title	Co-crystal of broadly neutralizing VHH in complex with short neurotoxin 1 (P01426) Naja pallida
Keywords keywords	nanobody, VHH, antibody, toxin, snake toxin, snake venom, neutralizing; TOXIN
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.

9riu__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9riu__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9riu__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.90 Å
Rg (electron density)	16.91 Å
Total Rg	17.85 Å
Atom count	2796
Residues	188
Excluded volume	25093 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9riu__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9riu__assembly_2__model_1`	dimeric （2）	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	Variable Domain of Heavy-Chain only Antibody (VHH)
Molecular weight formula_weight	13900.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	5627

QVQLQESGGGLVRPGGSLRLSCAVSGVSESIFANYVVGWFRQQDSGTGRDLVAQSSSDDEYNHVSGSVKGRFTISRDNAKNTVSLQMDNLKPEDTAIYICAAAIGPGDNYIYWGQGTQVTVSSENLYFQ

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Short neurotoxin 1
Molecular weight formula_weight	6805.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

LECHNQQSSQPPTTKTCPGETNCYKKVWRDHRGTIIERGCGCPTVKPGIKLNCCTTDKCNN

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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Unit-cell length a length_a	104.150 Å
Unit-cell length b length_b	104.090 Å
Unit-cell length c length_c	79.340 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	16

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	23.290 Å
R factor r_factor	0.3258
R_work r_work	0.3238
R_free r_free	0.3610

Co-crystal of broadly neutralizing VHH in complex with short neurotoxin 1 (P01426) Naja pallida

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

9riu__assembly_2__model_1

9riu__assembly_2__model_1 | I(q)

9riu__assembly_2__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Co-crystal of broadly neutralizing VHH in complex with short neurotoxin 1 (P01426) Naja pallida

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

9riu__assembly_2__model_1

9riu__assembly_2__model_1 | I(q)

9riu__assembly_2__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)