SAXSdb — 6ke5

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

Ion transport protein

Arcobacter butzleri RM4018

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE × 3 CALCIUM ION × 3 SN-GLYCEROL-3-PHOSPHATE × 5 amlodipine × 1 [(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate × 1 water × 1	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 18–284； UniProt 1–267 Author chain B； PDBConstruct 18–284； UniProt 1–267 Author chain C； PDBConstruct 18–284； UniProt 1–267 Author chain D； PDBConstruct 18–284； UniProt 1–267

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	6ke5
Deposition date deposition_date	2019-07-03
Structure title title	Structure of CavAb in complex with Diltiazem and Amlodipine
Keywords keywords	Voltage gated Ion Channel, Voltage-gated Calcium Channel, Block, Tetrameric, MEMBRANE PROTEIN; MEMBRANE 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.

6ke5__assembly_1__model_1

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

Download this curve (.dat)

6ke5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ke5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.85 Å
Rg (electron density)	33.11 Å
Total Rg	33.70 Å
Atom count	7575
Residues	902
Excluded volume	140500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ke5__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 (7)

Entity 1 Entity 1 polymer

Description description	Ion transport protein
Molecular weight formula_weight	32957.8 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	7576

DYKDDDDKGSLVPRGSHMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLDDWSNGIVRPLMEVYPYAYVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSLKN

Source Source

Source organism organism	Arcobacter butzleri RM4018
NCBI taxonomy ID ncbi_taxonomy_id	367737
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 non-polymer

Description description	[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE
Molecular weight formula_weight	468.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SN-GLYCEROL-3-PHOSPHATE
Molecular weight formula_weight	172.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	amlodipine
Molecular weight formula_weight	408.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	[(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6ke5a_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.14 — Gated ion channels
Superfamily Superfamily superfamily	f.14.1 — Voltage-gated ion channels
Family Family family	f.14.1.2 — Voltage-gated Na/Ca cation channels

Domain ID domain_id	d6ke5b_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.14 — Gated ion channels
Superfamily Superfamily superfamily	f.14.1 — Voltage-gated ion channels
Family Family family	f.14.1.2 — Voltage-gated Na/Ca cation channels

Domain ID domain_id	d6ke5c_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.14 — Gated ion channels
Superfamily Superfamily superfamily	f.14.1 — Voltage-gated ion channels
Family Family family	f.14.1.2 — Voltage-gated Na/Ca cation channels

Domain ID domain_id	d6ke5d_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.14 — Gated ion channels
Superfamily Superfamily superfamily	f.14.1 — Voltage-gated ion channels
Family Family family	f.14.1.2 — Voltage-gated Na/Ca cation channels

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Unit-cell length a length_a	124.730 Å
Unit-cell length b length_b	124.990 Å
Unit-cell length c length_c	191.940 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 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.803 Å
Low-resolution limit resolution_low	44.706 Å
R factor r_factor	0.2522
R_work r_work	0.2486
R_free r_free	0.2921

Structure of CavAb in complex with Diltiazem and Amlodipine

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

Ion transport protein

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

6ke5__assembly_1__model_1

6ke5__assembly_1__model_1 | I(q)

6ke5__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 (7)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)

Structure of CavAb in complex with Diltiazem and Amlodipine

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

Ion transport protein

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

6ke5__assembly_1__model_1

6ke5__assembly_1__model_1 | I(q)

6ke5__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 (7)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)