SAXSdb — 6v4s

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

Neur_chan_LBD domain-containing protein

uncultured Desulfofustis sp. PB-SRB1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	CALCIUM ION × 5 SODIUM ION × 7 CHLORIDE ION × 5 DODECYL-BETA-D-MALTOSIDE × 10 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	V4JF97_9DELT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–642； UniProt 1–642 Author chain B； PDBConstruct 1–642； UniProt 1–642 Author chain C； PDBConstruct 1–642； UniProt 1–642 Author chain D； PDBConstruct 1–642； UniProt 1–642 Author chain E； PDBConstruct 1–642； UniProt 1–642

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	6v4s
Deposition date deposition_date	2019-11-29
Structure title title	A Closed pore conformation of a Pentameic ligand-gated ion channel with additional N-terminal domain
Keywords keywords	Pentameric ligand-gated ion channel, 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.

6v4s__assembly_1__model_1

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

Download this curve (.dat)

6v4s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6v4s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.64 Å
Rg (electron density)	49.50 Å
Total Rg	49.83 Å
Atom count	23256
Residues	2941
Excluded volume	415720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6v4s__assembly_1__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Neur_chan_LBD domain-containing protein
Molecular weight formula_weight	71734.0 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,D,C,B
Atom count atom_count	23261

MHNLQQLLPTRSLIWIFSFLTSISIWCTVAHAETEGRVQHFTGYIEDGRGIFYSLPDMKQGDIIYASMQNTGGNLDPLVGIMAEEIDPAVSLGQVLEKALASENDLISELTAVADRIFLGWDDDGGKGYSASLEFTIPRDGTYHIFAGSTITNQRLDKFQPTYTTGSFQLILGLNAPQVISGEGEPEGEVFASLASLEIKPEAHVQELEIRLDKDTRYLTQHTRNLQPGDTFHALVEPIGEAPLPRLRLTDSGGKPLAFGLIDQPGESVELNYTCDQDICELVVHVDGTDGQKDSGEAVYRLLVGINAPNLRESGQTPVGSSVFLESDLVTVGLAVDQIVGVDQRSENFSVVGTLKLSWHDPKLGFSPDQCGCTVKSFEDASIRAVAGEINLPLPSFSFYNQQGNRWSQNQVIFVTPDGRASYFERFTVTLQAPDFDFLAYPFDRQKFSIKVDLAVPTNMFIFNEIERFQQVVGDQLGEEEWVVTSYSQEITEVPFERGSTNSRFTTTLLVKRNLEYYILRIFVPLFLIISVSWVIFFLKDYGRQLEVASGNLLVFVAFNFTISGDLPRLGYLTVLDRFMIVSFCLTAIVVLISVCQKRLGAVGKQAVAAQIDTWVLVIYPLVYSLYIIWVYLRFFTDHIGW

Source Source

Source organism organism	uncultured Desulfofustis sp. PB-SRB1
NCBI taxonomy ID ncbi_taxonomy_id	1385624
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	5

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	nat
Copy count entity_count	10

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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Unit-cell length a length_a	159.406 Å
Unit-cell length b length_b	337.254 Å
Unit-cell length c length_c	111.812 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	20

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.550 Å
Low-resolution limit resolution_low	48.040 Å
R factor r_factor	0.1972
R_work r_work	0.1935
R_free r_free	0.2681

A Closed pore conformation of a Pentameic ligand-gated ion channel with additional N-terminal domain

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

Neur_chan_LBD domain-containing 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

6v4s__assembly_1__model_1

6v4s__assembly_1__model_1 | I(q)

6v4s__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 (6)

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 water

7. Citations (1)

A Closed pore conformation of a Pentameic ligand-gated ion channel with additional N-terminal domain

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

Neur_chan_LBD domain-containing 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

6v4s__assembly_1__model_1

6v4s__assembly_1__model_1 | I(q)

6v4s__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 (6)

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 water

7. Citations (1)