2bwb

Crystal structure of the UBA domain of Dsk2 from S. cerevisiae

Method: X-RAY DIFFRACTION

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

UBIQUITIN-LIKE PROTEIN DSK2

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	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DSK2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–46； UniProt 326–371 Author chain B； PDBConstruct 1–46； UniProt 326–371 Author chain C； PDBConstruct 1–46； UniProt 326–371 Author chain D； PDBConstruct 1–46； UniProt 326–371 Author chain E； PDBConstruct 1–46； UniProt 326–371 Author chain F； PDBConstruct 1–46； UniProt 326–371 Author chain G； PDBConstruct 1–46； UniProt 326–371 Author chain H； PDBConstruct 1–46； UniProt 326–371 Author chain I； PDBConstruct 1–46； UniProt 326–371

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	2bwb
Deposition date deposition_date	2005-07-13
Structure title title	Crystal structure of the UBA domain of Dsk2 from S. cerevisiae
Keywords keywords	UBIQUITIN, UBA, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

2bwb__assembly_1__model_1

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

Download this curve (.dat)

2bwb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bwb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	11.24 Å
Rg (electron density)	9.73 Å
Total Rg	11.22 Å
Atom count	366
Residues	46
Excluded volume	6313 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bwb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bwb__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2bwb__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2bwb__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2bwb__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2bwb__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2bwb__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2bwb__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2bwb__assembly_9__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 (2)

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2bwba_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbb_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbc_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbd_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbe_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbf_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbg_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbh_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbi_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

CATH v4.4 (9 domains)

Domain ID domain_id	2bwbA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbI00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

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Unit-cell length a length_a	116.311 Å
Unit-cell length b length_b	44.069 Å
Unit-cell length c length_c	111.525 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	101.020 Å
R factor r_factor	0.2460
R_work r_work	0.2430
R_free r_free	0.3070

Description description	UBIQUITIN-LIKE PROTEIN DSK2
Molecular weight formula_weight	5214.7 kDa
Source method src_method	man
Copy count entity_count	9

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I
Atom count atom_count	3337

Crystal structure of the UBA domain of Dsk2 from S. cerevisiae

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

UBIQUITIN-LIKE PROTEIN DSK2

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

2bwb__assembly_1__model_1

2bwb__assembly_1__model_1 | I(q)

2bwb__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Source organism organism	SACCHAROMYCES CEREVISIAE
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	150

Crystal structure of the UBA domain of Dsk2 from S. cerevisiae

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

UBIQUITIN-LIKE PROTEIN DSK2

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

2bwb__assembly_1__model_1

2bwb__assembly_1__model_1 | I(q)

2bwb__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)