SAXSdb — 5fvk

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

VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	VPS4-ASSOCIATED PROTEIN 1 × 1 （P40080） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	VPS4-ASSOCIATED PROTEIN 1 × 1 （P40080） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–82； UniProt 1–82 Author chain B； PDBConstruct 1–82； UniProt 1–82

VPS4-ASSOCIATED PROTEIN 1

SACCHAROMYCES CEREVISIAE

UniProt P40080

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4 × 1 （P52917） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4 × 1 （P52917） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VFA1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–22； UniProt 182–203 Author chain D； PDBConstruct 1–22； UniProt 182–203

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	5fvk
Deposition date deposition_date	2016-02-09
Structure title title	Crystal structure of Vps4-Vfa1 complex from S.cerevisiae at 1.66 A resolution.
Keywords keywords	HYDROLASE, VPS4, VFA1, MIT DOMAIN, YEAST, ATPASE; HYDROLASE
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.

5fvk__assembly_2__model_1

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

Download this curve (.dat)

5fvk__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5fvk__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	16.18 Å
Rg (electron density)	15.00 Å
Total Rg	16.05 Å
Atom count	820
Residues	101
Excluded volume	14635 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5fvk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5fvk__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 (3)

Entity 1 Entity 1 polymer

Description description	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
Molecular weight formula_weight	9440.6 kDa
EC 编号 ec_number	3.6.4.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1785

MSTGDFLTKGIELVQKAIDLDTATQYEEAYTAYYNGLDYLMLALKYEKNPKSKDLIRAKFTEYLNRAEQLKKHLESEEANAA

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	VPS4-ASSOCIATED PROTEIN 1
Molecular weight formula_weight	2603.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ENYSNTDPEELLRKHVFPSVPK

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5fvka_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.14 — MIT domain
Family Family family	a.7.14.0 — automated matches

Domain ID domain_id	d5fvkb_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.14 — MIT domain
Family Family family	a.7.14.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5fvkA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

Domain ID domain_id	5fvkB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

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Unit-cell length a length_a	38.830 Å
Unit-cell length b length_b	56.460 Å
Unit-cell length c length_c	84.250 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	1.658 Å
Low-resolution limit resolution_low	31.994 Å
R factor r_factor	0.1857
R_work r_work	0.1837
R_free r_free	0.2223

Crystal structure of Vps4-Vfa1 complex from S.cerevisiae at 1.66 A resolution.

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

VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4

State in the Current Structure

Other States of the Same Protein in the Database

VPS4-ASSOCIATED PROTEIN 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

5fvk__assembly_2__model_1

5fvk__assembly_2__model_1 | I(q)

5fvk__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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)

Crystal structure of Vps4-Vfa1 complex from S.cerevisiae at 1.66 A resolution.

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

VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

VPS4-ASSOCIATED PROTEIN 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

5fvk__assembly_2__model_1

5fvk__assembly_2__model_1 | I(q)

5fvk__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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)