SAXSdb — 2v9b

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

VISCOTOXIN-B

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THNB_VISAL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–46； UniProt 7–52 Author chain B； PDBConstruct 1–46； UniProt 7–52

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	2v9b
Deposition date deposition_date	2007-08-23
Structure title title	X-ray structure of viscotoxin B2 from Viscum album
Keywords keywords	TOXIN, THIONIN, SECRETED, PLANT TOXIN, PLANT DEFENSE; 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.

2v9b__assembly_1__model_1

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

Download this curve (.dat)

2v9b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v9b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.48 Å
Rg (electron density)	14.05 Å
Total Rg	14.86 Å
Atom count	694
Residues	92
Excluded volume	11954 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v9b__assembly_1__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 (3)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2v9ba_
Class class	g — Small proteins
Fold Fold fold	g.13 — Crambin-like
Superfamily Superfamily superfamily	g.13.1 — Crambin-like
Family Family family	g.13.1.1 — Crambin-like

Domain ID domain_id	d2v9bb_
Class class	g — Small proteins
Fold Fold fold	g.13 — Crambin-like
Superfamily Superfamily superfamily	g.13.1 — Crambin-like
Family Family family	g.13.1.1 — Crambin-like

CATH v4.4 (2 domains)

Domain ID domain_id	2v9bA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	10 — Thionin-like

Domain ID domain_id	2v9bB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	10 — Thionin-like

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Unit-cell length a length_a	39.819 Å
Unit-cell length b length_b	40.392 Å
Unit-cell length c length_c	44.694 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.050 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	0.1703

Description description	VISCOTOXIN-B
Molecular weight formula_weight	4865.5 kDa
Mutation mutation	YES
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	835

X-ray structure of viscotoxin B2 from Viscum album

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

VISCOTOXIN-B

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

2v9b__assembly_1__model_1

2v9b__assembly_1__model_1 | I(q)

2v9b__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	106

X-ray structure of viscotoxin B2 from Viscum album

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

VISCOTOXIN-B

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

2v9b__assembly_1__model_1

2v9b__assembly_1__model_1 | I(q)

2v9b__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)