3u8l

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3570 (1-(5-phenylpyridin-3-yl)-1,4-diazepane)

Method: X-RAY DIFFRACTION

▼

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

Acetylcholine-binding protein

Lymnaea stagnalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	1-(5-phenylpyridin-3-yl)-1,4-diazepane × 7 SULFATE ION × 2 water × 5	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 5	1-(5-phenylpyridin-3-yl)-1,4-diazepane × 7 SULFATE ION × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACHP_LYMST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 20–229 Author chain B； PDBConstruct 1–210； UniProt 20–229 Author chain C； PDBConstruct 1–210； UniProt 20–229 Author chain D； PDBConstruct 1–210； UniProt 20–229 Author chain E； PDBConstruct 1–210； UniProt 20–229 Author chain F； PDBConstruct 1–210； UniProt 20–229 Author chain G； PDBConstruct 1–210； UniProt 20–229 Author chain H； PDBConstruct 1–210； UniProt 20–229 Author chain I； PDBConstruct 1–210； UniProt 20–229 Author chain J； PDBConstruct 1–210； UniProt 20–229

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3u8l
Deposition date deposition_date	2011-10-17
Structure title title	Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3570 (1-(5-phenylpyridin-3-yl)-1,4-diazepane)
Keywords keywords	;Lymnaea stagnalis, agonist, Ligand-bindig domain, Acetylcholine, Acetylcholine-binding protein, Acetylcholine-binding protein-agonist complex ;; Acetylcholine-binding protein/agonist
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3u8l__assembly_1__model_1

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

Download this curve (.dat)

3u8l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3u8l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.49 Å
Rg (electron density)	29.71 Å
Total Rg	30.61 Å
Atom count	8235
Residues	1013
Excluded volume	144600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3u8l__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3u8l__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Acetylcholine-binding protein
Molecular weight formula_weight	23862.5 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	17072

LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSEIL

Source Source

Source organism organism	Lymnaea stagnalis
Common name common_name	Great pond snail
NCBI taxonomy ID ncbi_taxonomy_id	6523
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	1-(5-phenylpyridin-3-yl)-1,4-diazepane
Molecular weight formula_weight	253.3 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	599

▼

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3u8la_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

Domain ID domain_id	d3u8lb_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

Domain ID domain_id	d3u8lc_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

Domain ID domain_id	d3u8ld_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

Domain ID domain_id	d3u8le_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

Domain ID domain_id	d3u8lf_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

Domain ID domain_id	d3u8lg_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

Domain ID domain_id	d3u8lh_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

Domain ID domain_id	d3u8li_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

Domain ID domain_id	d3u8lj_
Class class	b — All beta proteins
Fold Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
Family Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

CATH v4.4 (10 domains)

Domain ID domain_id	3u8lA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	3u8lB00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	3u8lC00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	3u8lD00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	3u8lE00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	3u8lF00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	3u8lG00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	3u8lH00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	3u8lI00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	3u8lJ00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

▶

Unit-cell length a length_a	73.960 Å
Unit-cell length b length_b	114.810 Å
Unit-cell length c length_c	127.060 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.320 Å
Low-resolution limit resolution_low	42.346 Å
R factor r_factor	0.1932
R_work r_work	0.1906
R_free r_free	0.2441

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3570 (1-(5-phenylpyridin-3-yl)-1,4-diazepane)

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

Acetylcholine-binding 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

3u8l__assembly_1__model_1

3u8l__assembly_1__model_1 | I(q)

3u8l__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 (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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3570 (1-(5-phenylpyridin-3-yl)-1,4-diazepane)

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

Acetylcholine-binding 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

3u8l__assembly_1__model_1

3u8l__assembly_1__model_1 | I(q)

3u8l__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 (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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)