SAXSdb — 3gin

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

Sodium/calcium exchanger 1

Canis lupus familiaris

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 4 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAC1_CANFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–160； UniProt 402–541 Author chain B； PDBConstruct 21–160； UniProt 402–541

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	3gin
Deposition date deposition_date	2009-03-05
Structure title title	Crystal structure of E454K-CBD1
Keywords keywords	;CBD1, CBD2, NCX, calcium binding domain 1, Antiport, Calcium transport, Calmodulin-binding, Cell membrane, Glycoprotein, Ion transport, Membrane, Phosphoprotein, Sodium transport, Transmembrane, Transport, METAL TRANSPORT, METAL BINDING PROTEIN ;; METAL BINDING 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.

3gin__assembly_1__model_1

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

Download this curve (.dat)

3gin__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gin__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.53 Å
Rg (electron density)	15.73 Å
Total Rg	16.75 Å
Atom count	899
Residues	116
Excluded volume	16005 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gin__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gin__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Sodium/calcium exchanger 1
Molecular weight formula_weight	17462.2 kDa
Mutation mutation	E454K
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	1896

MAHHHHHHSAALEVLFQGPGPVSKIFFEQGTYQCLENCGTVALTIIRRGGDLTNTVFVDFRTEDGTANAGSDYEFTEGTVVFKPGETQKEIRVGIIDDDIFEEDKNFLVHLSNVKVSSEASEDGILEANHVSALACLGSPSTATVTIFDDDHAGIFTFEE

Source Source

Source organism organism	Canis lupus familiaris
Common name common_name	dog
NCBI taxonomy ID ncbi_taxonomy_id	9615
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3gina_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.27 — CalX-like
Family Family family	b.1.27.1 — CalX-beta domain

Domain ID domain_id	d3ginb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.27 — CalX-like
Family Family family	b.1.27.1 — CalX-beta domain

CATH v4.4 (2 domains)

Domain ID domain_id	3ginA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2030 — CalX-beta domain

Domain ID domain_id	3ginB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2030 — CalX-beta domain

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Unit-cell length a length_a	91.858 Å
Unit-cell length b length_b	91.858 Å
Unit-cell length c length_c	65.590 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	64.960 Å
R factor r_factor	0.1961
R_work r_work	0.1930
R_free r_free	0.2586

Crystal structure of E454K-CBD1

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

Sodium/calcium exchanger 1

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

3gin__assembly_1__model_1

3gin__assembly_1__model_1 | I(q)

3gin__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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of E454K-CBD1

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

Sodium/calcium exchanger 1

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

3gin__assembly_1__model_1

3gin__assembly_1__model_1 | I(q)

3gin__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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)