SAXSdb — 5iiq

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

Vacuolar transporter chaperone 4

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 3 PYROPHOSPHATE 2- × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VTC4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–483； UniProt 2–480

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	5iiq
Deposition date deposition_date	2016-03-01
Structure title title	Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B).
Keywords keywords	helical bundle, alpha-helical hairpin, inositol phosphate binding, protein-protein interaction, chaperone, transferase; TRANSFERASE
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.

5iiq__assembly_1__model_1

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

Download this curve (.dat)

5iiq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5iiq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.75 Å
Rg (electron density)	41.30 Å
Total Rg	41.22 Å
Atom count	3807
Residues	463
Excluded volume	67445 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5iiq__assembly_1__model_1`	monomeric （1）	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 transporter chaperone 4
Molecular weight formula_weight	56951.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3807

GAMGKFGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGQWTQELETDFLESLEIELDKVYTFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDFEILEEELSDIIADVHDLAKFSRLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTSGRPIKGDSSAGGKQQNFVRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLPQGS

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5iiqA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	30 — VTC, catalytic tunnel domain

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Unit-cell length a length_a	92.041 Å
Unit-cell length b length_b	92.041 Å
Unit-cell length c length_c	301.732 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	3.030 Å
Low-resolution limit resolution_low	19.880 Å
R factor r_factor	0.2266
R_work r_work	0.2246
R_free r_free	0.2624

Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B).

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

Vacuolar transporter chaperone 4

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

5iiq__assembly_1__model_1

5iiq__assembly_1__model_1 | I(q)

5iiq__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B).

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

Vacuolar transporter chaperone 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5iiq__assembly_1__model_1

5iiq__assembly_1__model_1 | I(q)

5iiq__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)