SAXSdb — 5ek0

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

Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha

Arcobacter butzleri, Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 4	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 21 3-cyano-4-[2-[2-(1-ethylazetidin-3-yl)pyrazol-3-yl]-4-(trifluoromethyl)phenoxy]-~{N}-(1,2,4-thiadiazol-5-yl)benzenesulfonamide × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8EVM5_ARCB4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–41； UniProt 1–23 Author chain A； PDBConstruct 75–95； UniProt 58–78 Author chain A； PDBConstruct 138–296； UniProt 109–267 Author chain B； PDBConstruct 19–41； UniProt 1–23 Author chain B； PDBConstruct 75–95； UniProt 58–78 Author chain B； PDBConstruct 138–296； UniProt 109–267 Author chain C； PDBConstruct 19–41； UniProt 1–23 Author chain C； PDBConstruct 75–95； UniProt 58–78 Author chain C； PDBConstruct 138–296； UniProt 109–267 Author chain D； PDBConstruct 19–41； UniProt 1–23 Author chain D； PDBConstruct 75–95； UniProt 58–78 Author chain D； PDBConstruct 138–296； UniProt 109–267

Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha

Arcobacter butzleri, Homo sapiens

UniProt Q15858

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 4	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 21 3-cyano-4-[2-[2-(1-ethylazetidin-3-yl)pyrazol-3-yl]-4-(trifluoromethyl)phenoxy]-~{N}-(1,2,4-thiadiazol-5-yl)benzenesulfonamide × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCN9A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 42–74； UniProt 1527–1559 Author chain A； PDBConstruct 96–137； UniProt 1581–1622 Author chain B； PDBConstruct 42–74； UniProt 1527–1559 Author chain B； PDBConstruct 96–137； UniProt 1581–1622 Author chain C； PDBConstruct 42–74； UniProt 1527–1559 Author chain C； PDBConstruct 96–137； UniProt 1581–1622 Author chain D； PDBConstruct 42–74； UniProt 1527–1559 Author chain D； PDBConstruct 96–137； UniProt 1581–1622

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	5ek0
Deposition date deposition_date	2015-11-03
Structure title title	Human Nav1.7-VSD4-NavAb in complex with GX-936.
Keywords keywords	membrane protein, ion channel, voltage-gated sodium channel, small molecule antagonist, METAL TRANSPORT; METAL TRANSPORT
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.

5ek0__assembly_1__model_1

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

Download this curve (.dat)

5ek0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ek0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.44 Å
Rg (electron density)	34.55 Å
Total Rg	34.97 Å
Atom count	8571
Residues	979
Excluded volume	159470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ek0__assembly_1__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha
Molecular weight formula_weight	34618.1 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	8571

MDYKDDDDKGSLVPRGSHMYLRITNIVESSFFTKFIIYLIVLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTIEIILRIYVHRISFFKDPWSLFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSLKN

Source Source

Source organism organism	Arcobacter butzleri, Homo sapiens
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 non-polymer

Description description	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	678.9 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 3 Entity 3 non-polymer

Description description	3-cyano-4-[2-[2-(1-ethylazetidin-3-yl)pyrazol-3-yl]-4-(trifluoromethyl)phenoxy]-~{N}-(1,2,4-thiadiazol-5-yl)benzenesulfonamide
Molecular weight formula_weight	575.6 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5ek0A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	350 — Voltage-gated potassium channels. Chain C

Domain ID domain_id	5ek0A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5ek0B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	350 — Voltage-gated potassium channels. Chain C

Domain ID domain_id	5ek0B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5ek0C01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	350 — Voltage-gated potassium channels. Chain C

Domain ID domain_id	5ek0C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5ek0D01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	350 — Voltage-gated potassium channels. Chain C

Domain ID domain_id	5ek0D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

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Unit-cell length a length_a	169.420 Å
Unit-cell length b length_b	188.830 Å
Unit-cell length c length_c	171.130 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.530 Å
Low-resolution limit resolution_low	26.590 Å
R factor r_factor	0.2442
R_work r_work	0.2427
R_free r_free	0.2719

Human Nav1.7-VSD4-NavAb in complex with GX-936.

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

Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha

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

5ek0__assembly_1__model_1

5ek0__assembly_1__model_1 | I(q)

5ek0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Human Nav1.7-VSD4-NavAb in complex with GX-936.

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

Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha

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

5ek0__assembly_1__model_1

5ek0__assembly_1__model_1 | I(q)

5ek0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)