SAXSdb — 2ftx

▼

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

Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region

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	Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region × 1 （Q04477） SODIUM ION × 1 PHOSPHATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YEK8_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–90； UniProt 133–221

Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region

Saccharomyces cerevisiae

UniProt Q04477

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region × 1 （P40014） SODIUM ION × 1 PHOSPHATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YM06_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–64； UniProt 154–213

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ftx
Deposition date deposition_date	2006-01-25
Structure title title	Crystal structure of the yeast kinetochore Spc24/Spc25 globular domain
Keywords keywords	alpha-beta, complex, coiled-coil, structural protein, protein binding; structural protein, protein binding
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2ftx__assembly_1__model_1

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

Download this curve (.dat)

2ftx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ftx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.94 Å
Rg (electron density)	15.37 Å
Total Rg	16.46 Å
Atom count	1188
Residues	146
Excluded volume	21226 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ftx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region
Molecular weight formula_weight	10030.0 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	1267

MNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

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	Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region
Molecular weight formula_weight	7532.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHMEANENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK

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 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	79

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ftxa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.300 — Kinetochore globular domain-like
Superfamily Superfamily superfamily	d.300.1 — Kinetochore globular domain
Family Family family	d.300.1.1 — Spc25-like

Domain ID domain_id	d2ftxb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.300 — Kinetochore globular domain-like
Superfamily Superfamily superfamily	d.300.1 — Kinetochore globular domain
Family Family family	d.300.1.2 — Spc24-like

CATH v4.4 (2 domains)

Domain ID domain_id	2ftxA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily	50 — Chromosome segregation protein Spc25

Domain ID domain_id	2ftxB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	430 —

▶

Unit-cell length a length_a	84.907 Å
Unit-cell length b length_b	84.907 Å
Unit-cell length c length_c	93.195 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	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2100
R_work r_work	0.2090
R_free r_free	0.2260

Crystal structure of the yeast kinetochore Spc24/Spc25 globular domain

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

Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region

State in the Current Structure

Other States of the Same Protein in the Database

Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region

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

2ftx__assembly_1__model_1

2ftx__assembly_1__model_1 | I(q)

2ftx__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the yeast kinetochore Spc24/Spc25 globular domain

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

Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region

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

2ftx__assembly_1__model_1

2ftx__assembly_1__model_1 | I(q)

2ftx__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)