SAXSdb — 1kvd

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

SMK TOXIN

OrganismNot specified

UniProt P19972

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 × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 3 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 8	SULFATE ION × 14 water × 8	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 7 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOXK_PICFA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–63； UniProt 19–81 Author chain C； PDBConstruct 1–63； UniProt 19–81 Author chain B； PDBConstruct 1–77； UniProt 146–222 Author chain D； PDBConstruct 1–77； UniProt 146–222

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	1kvd
Deposition date deposition_date	1996-10-04
Structure title title	KILLER TOXIN FROM HALOTOLERANT YEAST
Keywords keywords	TOXIN, HALOTOLERANT YEAST; 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.

1kvd__assembly_1__model_1

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

Download this curve (.dat)

1kvd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kvd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.10 Å
Rg (electron density)	13.72 Å
Total Rg	14.87 Å
Atom count	1014
Residues	140
Excluded volume	17609 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kvd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1kvd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1kvd__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1kvd__assembly_4__model_1`	tetrameric （4）	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	SMK TOXIN
Molecular weight formula_weight	6349.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2247

WSLRWRMQKSTTIAAIAGCSGAATFGGLAGGIVGCIAAGILAILQGFEVNWHNGGGGDRSNPV

Entity 2 Entity 2 polymer

Description description	SMK TOXIN
Molecular weight formula_weight	7856.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

GEATTIWGVGADEAIDKGTPSKNDLQNMSADLAKNGFKGHQGVACSTVKDGNKDVYMIKFSLAGGSNDPGGSPCSDD

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1kvd.1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.70 — Yeast killer toxins
Superfamily Superfamily superfamily	d.70.1 — Yeast killer toxins
Family Family family	d.70.1.2 — SMK toxin

Domain ID domain_id	d1kvd.2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.70 — Yeast killer toxins
Superfamily Superfamily superfamily	d.70.1 — Yeast killer toxins
Family Family family	d.70.1.2 — SMK toxin

CATH v4.4 (4 domains)

Domain ID domain_id	1kvdA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	420 — Smk Toxin, alpha chain
Homologous superfamily homologous superfamily	10 — Smk Toxin, alpha chain

Domain ID domain_id	1kvdB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	44 — Smk Toxin, Beta chain
Homologous superfamily homologous superfamily	10 — Smk Toxin, beta chain

Domain ID domain_id	1kvdC00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	420 — Smk Toxin, alpha chain
Homologous superfamily homologous superfamily	10 — Smk Toxin, alpha chain

Domain ID domain_id	1kvdD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	44 — Smk Toxin, Beta chain
Homologous superfamily homologous superfamily	10 — Smk Toxin, beta chain

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Unit-cell length a length_a	81.100 Å
Unit-cell length b length_b	81.100 Å
Unit-cell length c length_c	118.460 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	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.1860
R_free r_free	—

KILLER TOXIN FROM HALOTOLERANT YEAST

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

SMK TOXIN

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

1kvd__assembly_1__model_1

1kvd__assembly_1__model_1 | I(q)

1kvd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)

KILLER TOXIN FROM HALOTOLERANT YEAST

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

SMK TOXIN

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

1kvd__assembly_1__model_1

1kvd__assembly_1__model_1 | I(q)

1kvd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)