SAXSdb — 3dh4

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

Sodium/glucose cotransporter

Vibrio parahaemolyticus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	beta-D-galactopyranose × 4 ERBIUM (III) ION × 4 SODIUM ION × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	beta-D-galactopyranose × 2 ERBIUM (III) ION × 2 SODIUM ION × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	beta-D-galactopyranose × 2 ERBIUM (III) ION × 2 SODIUM ION × 2	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	beta-D-galactopyranose × 1 ERBIUM (III) ION × 2 SODIUM ION × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	beta-D-galactopyranose × 1 SODIUM ION × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	beta-D-galactopyranose × 1 SODIUM ION × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	beta-D-galactopyranose × 1 ERBIUM (III) ION × 2 SODIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SGLT_VIBPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–514； UniProt 47–543 Author chain B； PDBConstruct 18–514； UniProt 47–543 Author chain C； PDBConstruct 18–514； UniProt 47–543 Author chain D； PDBConstruct 18–514； UniProt 47–543

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	3dh4
Deposition date deposition_date	2008-06-16
Structure title title	Crystal Structure of Sodium/Sugar symporter with bound Galactose from vibrio parahaemolyticus
Keywords keywords	;Membrane protein, symporter, sugar transport, SGLT, Ion transport, Membrane, Sodium transport, Symport, Transmembrane, Transport, TRANSPORT PROTEIN ;; TRANSPORT 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.

3dh4__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dh4__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dh4__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	24.19 Å
Rg (electron density)	22.93 Å
Total Rg	23.98 Å
Atom count	3869
Residues	512
Excluded volume	71199 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dh4__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dh4__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3dh4__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3dh4__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3dh4__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3dh4__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3dh4__assembly_7__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 (4)

Entity 1 Entity 1 polymer

Description description	Sodium/glucose cotransporter
Molecular weight formula_weight	56933.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15472

XXXXXXXXXXXXXXXXXAGKSLPWWAVGASLIAANISAEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLKTILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLSMPFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVTSSMFVTDRSFNIAAYGIMIVLAVLYTLFWVLYKSGGSPGHHHHHH

Source Source

Source organism organism	Vibrio parahaemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	670
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	beta-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ERBIUM (III) ION
Molecular weight formula_weight	167.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3dh4A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1730 — Sodium/glucose cotransporter
Homologous superfamily homologous superfamily	10 — Sodium/glucose cotransporter

Domain ID domain_id	3dh4B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1730 — Sodium/glucose cotransporter
Homologous superfamily homologous superfamily	10 — Sodium/glucose cotransporter

Domain ID domain_id	3dh4C01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1730 — Sodium/glucose cotransporter
Homologous superfamily homologous superfamily	10 — Sodium/glucose cotransporter

Domain ID domain_id	3dh4D01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1730 — Sodium/glucose cotransporter
Homologous superfamily homologous superfamily	10 — Sodium/glucose cotransporter

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Unit-cell length a length_a	83.280 Å
Unit-cell length b length_b	109.210 Å
Unit-cell length c length_c	127.580 Å
Unit-cell angle α angle_alpha	109.70 °
Unit-cell angle β angle_beta	92.02 °
Unit-cell angle γ angle_gamma	102.11 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2706
R_work r_work	0.2698
R_free r_free	0.2872

Crystal Structure of Sodium/Sugar symporter with bound Galactose from vibrio parahaemolyticus

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

Sodium/glucose cotransporter

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

3dh4__assembly_4__model_1

3dh4__assembly_4__model_1 | I(q)

3dh4__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Sodium/Sugar symporter with bound Galactose from vibrio parahaemolyticus

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

Sodium/glucose cotransporter

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

3dh4__assembly_4__model_1

3dh4__assembly_4__model_1 | I(q)

3dh4__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)