SAXSdb — 6fx4

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

E3 ubiquitin-protein ligase SMURF2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Polyubiquitin-B × 1 （P0CG47） GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Polyubiquitin-B × 1 （P0CG47） GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMUF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–119； UniProt 631–745 Author chain C； PDBConstruct 5–119； UniProt 631–745

Polyubiquitin-B

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase SMURF2 × 1 （Q9HAU4） GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase SMURF2 × 1 （Q9HAU4） GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76

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	6fx4
Deposition date deposition_date	2018-03-08
Structure title title	Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C
Keywords keywords	E3 HECT ligase, Ubiquitin transfer, LIGASE; LIGASE
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.

6fx4__assembly_1__model_1

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

Download this curve (.dat)

6fx4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6fx4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.43 Å
Rg (electron density)	18.55 Å
Total Rg	19.48 Å
Atom count	1554
Residues	192
Excluded volume	27773 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6fx4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6fx4__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 (4)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase SMURF2
Molecular weight formula_weight	13944.8 kDa
EC 编号 ec_number	2.3.2.26
Mutation mutation	C646A, C706N, C743S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3203

GAMGKIDVNDWKVNTRLKHATPDSNIVKWFWKAVEFFDEERRARLLQFVTGSSRVPLQGFKALQGAAGPRLFTIHQIDANTNNLPKAHTCFNRIDIPPYESYEKLYEKLLTAIEETSGFAVE

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 polymer

Description description	Polyubiquitin-B
Molecular weight formula_weight	8622.9 kDa
Mutation mutation	G76C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC

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 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6fx4b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6fx4d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (2 domains)

Domain ID domain_id	6fx4A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2410 — Hect, E3 ligase catalytic fold
Homologous superfamily homologous superfamily	10 — Hect, E3 ligase catalytic domain

Domain ID domain_id	6fx4C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2410 — Hect, E3 ligase catalytic fold
Homologous superfamily homologous superfamily	10 — Hect, E3 ligase catalytic domain

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Unit-cell length a length_a	38.630 Å
Unit-cell length b length_b	45.950 Å
Unit-cell length c length_c	70.460 Å
Unit-cell angle α angle_alpha	108.92 °
Unit-cell angle β angle_beta	94.43 °
Unit-cell angle γ angle_gamma	106.75 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.566 Å
R factor r_factor	0.1899
R_work r_work	0.1873
R_free r_free	0.2390

Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C

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

E3 ubiquitin-protein ligase SMURF2

State in the Current Structure

Other States of the Same Protein in the Database

Polyubiquitin-B

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

6fx4__assembly_1__model_1

6fx4__assembly_1__model_1 | I(q)

6fx4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C

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

E3 ubiquitin-protein ligase SMURF2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polyubiquitin-B

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

6fx4__assembly_1__model_1

6fx4__assembly_1__model_1 | I(q)

6fx4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)