3wip

Crystal structure of acetylcholine bound to Ls-AChBP

Method: X-RAY DIFFRACTION

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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	ACETYLCHOLINE × 5 PENTAETHYLENE GLYCOL × 8 SULFATE ION × 4 ACETATE ION × 1 water × 5	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 5	ACETYLCHOLINE × 5 PENTAETHYLENE GLYCOL × 4 SULFATE ION × 3 ACETATE ION × 2 GLYCEROL × 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 1–229； UniProt 1–229 Author chain B； PDBConstruct 1–229； UniProt 1–229 Author chain C； PDBConstruct 1–229； UniProt 1–229 Author chain D； PDBConstruct 1–229； UniProt 1–229 Author chain E； PDBConstruct 1–229； UniProt 1–229 Author chain F； PDBConstruct 1–229； UniProt 1–229 Author chain G； PDBConstruct 1–229； UniProt 1–229 Author chain H； PDBConstruct 1–229； UniProt 1–229 Author chain I； PDBConstruct 1–229； UniProt 1–229 Author chain J； PDBConstruct 1–229； UniProt 1–229

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3wip
Deposition date deposition_date	2013-09-24
Structure title title	Crystal structure of acetylcholine bound to Ls-AChBP
Keywords keywords	ACETYLCHOLINE-BINDING PROTEIN, Acetylcholine-binding protein-agonist complex, Lymnaea stagnalis, Agonist, Acetylcholine; ACETYLCHOLINE-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.

3wip__assembly_1__model_1

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

Download this curve (.dat)

3wip__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wip__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.57 Å
Rg (electron density)	29.77 Å
Total Rg	30.67 Å
Atom count	8319
Residues	1016
Excluded volume	147050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wip__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3wip__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	Acetylcholine-binding protein
Molecular weight formula_weight	26087.3 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	17146

MRRNIFCLACLWIVQACLSLDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSEIL

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	ACETYLCHOLINE
Molecular weight formula_weight	146.2 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	407

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3wipa_
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	d3wipb_
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	d3wipc_
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	d3wipd_
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	d3wipe_
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	d3wipf_
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	d3wipg_
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	d3wiph_
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	d3wipi_
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	d3wipj_
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	3wipA00
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	3wipB00
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	3wipC00
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	3wipD00
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	3wipE00
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	3wipF00
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	3wipG00
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	3wipH00
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	3wipI00
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	3wipJ00
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

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Unit-cell length a length_a	236.850 Å
Unit-cell length b length_b	73.150 Å
Unit-cell length c length_c	132.470 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	46.172 Å
R factor r_factor	0.1818
R_work r_work	0.1787
R_free r_free	0.2389

Crystal structure of acetylcholine bound to Ls-AChBP

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

3wip__assembly_1__model_1

3wip__assembly_1__model_1 | I(q)

3wip__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) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of acetylcholine bound to Ls-AChBP

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

3wip__assembly_1__model_1

3wip__assembly_1__model_1 | I(q)

3wip__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) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)