SAXSdb — 3sy2

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

E3 ubiquitin-protein ligase SopA

Salmonella enterica subsp. enterica serovar Typhimurium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SOPA_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–621； UniProt 165–782 Author chain B； PDBConstruct 4–621； UniProt 165–782

Ubiquitin-conjugating enzyme E2 L3

Homo sapiens

UniProt P68036

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 SopA × 1 （Q8ZNR3） SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase SopA × 1 （Q8ZNR3） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UB2L3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–156； UniProt 1–154 Author chain D； PDBConstruct 3–156； UniProt 1–154

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	3sy2
Deposition date deposition_date	2011-07-15
Structure title title	Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7
Keywords keywords	;pentapeptide, HECT domain, HECT E3, HECT E3 ubiquitin ligase, E2 ubiquitin conjugating enzyme, ubiquitin, protein-protein complex, effector protein, ubiquitin transfer, ubiquitination, LIGASE-SIGNALING PROTEIN complex ;; LIGASE/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.

3sy2__assembly_1__model_1

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

Download this curve (.dat)

3sy2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3sy2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.04 Å
Rg (electron density)	35.03 Å
Total Rg	35.16 Å
Atom count	5803
Residues	763
Excluded volume	102360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3sy2__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3sy2__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 SopA
Molecular weight formula_weight	69235.2 kDa
EC 编号 ec_number	6.3.2.-
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	11660

SNASSPSSPADWAKKLTDAVLRQKAGETLTAADRDFSNADFRNITFSKILPPSFMERDGDIIKGFNFSNSKFTYSDISHLHFDECRFTYSTLSDVVCSNTKFSNSDMNEVFLQYSITTQQQPSFIDTTLKNTLIRHKANLSGVILNEPDNSSPPSVSGGGNFIRLGDIWLQMPLLWTENAVDGFLNHEHNNGKSILMTIDSLPDKYSQEKVQAMEDLVKSLRGGRLTEACIRPVESSLVSVLAHPPYTQSALISEWLGPVQERFFAHQCQTYNDVPLPAPDTYYQQRILPVLLDSFDRNSAAMTTHSGLFNQVILHCMTGVDCTDGTRQKAAALYEQYLAHPAVSPHIHNGLFGNYDGSPDWTTRAADNFLLLSSQDSDTAMMLSTDTLLTMLNPTPDTAWDNFYLLRAGENVSTAQISPVELFRHDFPVFLAAFNQQATQRRFGELIDIILSTEEHGELNQQFLAATNQKHSTVKLIDDASVSRLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAIFGTEHDSPPALRGYAEALMQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSMQRHARKYFPSVLSSILPLAWA

Source Source

Source organism organism	Salmonella enterica subsp. enterica serovar Typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	90371
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin-conjugating enzyme E2 L3
Molecular weight formula_weight	18033.7 kDa
EC 编号 ec_number	6.3.2.19
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSMAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVD

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	SULFATE ION
Molecular weight formula_weight	96.1 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	15

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	3sy2A01
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	80 — E3 ubiquitin-protein ligase SopA

Domain ID domain_id	3sy2A02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	300 — Putative secreted effector protein

Domain ID domain_id	3sy2A03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1850 — HECT-like ubiquitin ligase fold
Homologous superfamily homologous superfamily	10 — HECT-like ubiquitin ligase

Domain ID domain_id	3sy2A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4140 — effector protein (NleL) fold
Homologous superfamily homologous superfamily	10 — effector protein (NleL)

Domain ID domain_id	3sy2B01
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	80 — E3 ubiquitin-protein ligase SopA

Domain ID domain_id	3sy2B02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	300 — Putative secreted effector protein

Domain ID domain_id	3sy2B03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1850 — HECT-like ubiquitin ligase fold
Homologous superfamily homologous superfamily	10 — HECT-like ubiquitin ligase

Domain ID domain_id	3sy2B04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4140 — effector protein (NleL) fold
Homologous superfamily homologous superfamily	10 — effector protein (NleL)

Domain ID domain_id	3sy2C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	3sy2D00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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Unit-cell length a length_a	74.120 Å
Unit-cell length b length_b	118.363 Å
Unit-cell length c length_c	241.671 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.270 Å
Low-resolution limit resolution_low	45.424 Å
R factor r_factor	0.2144
R_work r_work	0.2112
R_free r_free	0.2746

Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7

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

E3 ubiquitin-protein ligase SopA

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-conjugating enzyme E2 L3

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

3sy2__assembly_1__model_1

3sy2__assembly_1__model_1 | I(q)

3sy2__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) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7

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

E3 ubiquitin-protein ligase SopA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-conjugating enzyme E2 L3

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

3sy2__assembly_1__model_1

3sy2__assembly_1__model_1 | I(q)

3sy2__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) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)