SAXSdb — 3lmn

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

Ubiquitin carboxyl-terminal hydrolase 15

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	FORMIC ACID × 4 ACETIC ACID × 4 water × 8	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	FORMIC ACID × 2 ACETIC ACID × 2 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	FORMIC ACID × 1 ACETIC ACID × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	ACETIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP15_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–135； UniProt 1–133 Author chain B； PDBConstruct 3–135； UniProt 1–133

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	3lmn
Deposition date deposition_date	2010-01-31
Structure title title	Oligomeric structure of the DUSP domain of human USP15
Keywords keywords	;HYDROLASE, UCH, USP, DUB, DEUBIQUITYLATION, DEUBIQUITINATING ENZYME, UBIQUITIN, UBIQUITIN SPECIFIC PROTEASE, UBIQUITIN CARBOXYTERMINAL HYDROLASE, CLEAVAGE, USP15, DUB15, UBP15, ENDOPEPTIDASE, THIOLESTERASE, DUSP, DOMAIN-SWAPPING, STRUCTURAL GENOMICS CONSORTIUM (SGC), Acetylation, Alternative splicing, Phosphoprotein, Protease, Thiol protease, Ubl conjugation pathway ;; 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.

3lmn__assembly_2__model_1

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

Download this curve (.dat)

3lmn__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lmn__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.96 Å
Rg (electron density)	31.42 Å
Total Rg	31.86 Å
Atom count	4246
Residues	520
Excluded volume	75819 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lmn__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lmn__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3lmn__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3lmn__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 15
Molecular weight formula_weight	15528.6 kDa
EC 编号 ec_number	3.1.2.15
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	2373

GSMAEGGAADLDTQRSDIATLLKTSLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGLLKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3lmna_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.324 — DUSP-like
Superfamily Superfamily superfamily	d.324.1 — DUSP-like
Family Family family	d.324.1.1 — DUSP, domain in ubiquitin-specific proteases

Domain ID domain_id	d3lmnb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.324 — DUSP-like
Superfamily Superfamily superfamily	d.324.1 — DUSP-like
Family Family family	d.324.1.1 — DUSP, domain in ubiquitin-specific proteases

CATH v4.4 (2 domains)

Domain ID domain_id	3lmnA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2230 — DUSP-like
Homologous superfamily homologous superfamily	10 — DUSP-like

Domain ID domain_id	3lmnB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2230 — DUSP-like
Homologous superfamily homologous superfamily	10 — DUSP-like

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Unit-cell length a length_a	138.174 Å
Unit-cell length b length_b	138.174 Å
Unit-cell length c length_c	132.114 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	32

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	19.520 Å
R factor r_factor	0.1844
R_work r_work	0.1834
R_free r_free	0.2040

Oligomeric structure of the DUSP domain of human USP15

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

Ubiquitin carboxyl-terminal hydrolase 15

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

3lmn__assembly_2__model_1

3lmn__assembly_2__model_1 | I(q)

3lmn__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Oligomeric structure of the DUSP domain of human USP15

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

Ubiquitin carboxyl-terminal hydrolase 15

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

3lmn__assembly_2__model_1

3lmn__assembly_2__model_1 | I(q)

3lmn__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)