SAXSdb — 8v13

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

Short neurotoxin 1

Dendraspis polylepis polylepis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Centi-SNX-B03 Fab heavy chain × 1 Centi-SNX-B03 Fab light chain × 1 SODIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Centi-SNX-B03 Fab heavy chain × 1 Centi-SNX-B03 Fab light chain × 1 SODIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	3S11_DENPO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain T； PDBConstruct 1–60； UniProt 1–60 Author chain t； PDBConstruct 1–60； UniProt 1–60

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	8v13
Deposition date deposition_date	2023-11-19
Structure title title	Crystal structure of Black mamba toxin in complex with Centi-SNX-B03 antibody
Keywords keywords	antivenom, 3-finger toxin, short neurotoxin, antibody, ANTITOXIN-IMMUNE SYSTEM complex; ANTITOXIN/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.

8v13__assembly_2__model_1

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

Download this curve (.dat)

8v13__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8v13__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.50 Å
Rg (electron density)	26.67 Å
Total Rg	27.55 Å
Atom count	3669
Residues	491
Excluded volume	64634 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8v13__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8v13__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 (5)

Entity 1 Entity 1 polymer

Description description	Centi-SNX-B03 Fab heavy chain
Molecular weight formula_weight	24222.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,h
Atom count atom_count	8271

QVQLQESGGGVVRPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDSSKNTLYLQINSLRAEDTALYYCAREGDYDSMDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Centi-SNX-B03 Fab light chain
Molecular weight formula_weight	22741.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SQSVVTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVFDDSARPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDNNSDDVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Short neurotoxin 1
Molecular weight formula_weight	6928.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T,t

RICYNHQSTTRATTKSCEENSCYKKYWRDHRGTIIERGCGCPKVKPGVGIHCCQSDKCNY

Source Source

Source organism organism	Dendraspis polylepis polylepis
Common name common_name	black mamba
NCBI taxonomy ID ncbi_taxonomy_id	8620
Host organism host_organism	Dendroaspis polylepis polylepis

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	860

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Unit-cell length a length_a	103.539 Å
Unit-cell length b length_b	72.252 Å
Unit-cell length c length_c	179.656 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	30.010 Å
R factor r_factor	0.1816
R_work r_work	0.1812
R_free r_free	0.2294

Crystal structure of Black mamba toxin in complex with Centi-SNX-B03 antibody

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

8v13__assembly_2__model_1

8v13__assembly_2__model_1 | I(q)

8v13__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of Black mamba toxin in complex with Centi-SNX-B03 antibody

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

8v13__assembly_2__model_1

8v13__assembly_2__model_1 | I(q)

8v13__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)