4zru

X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) in complex with 3-[2-[(2S)-pyrrolidin-2-yl]ethynyl]pyridine (TI-5180)

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	PHOSPHATE ION × 5 3-[(2S)-pyrrolidin-2-ylethynyl]pyridine × 5 water × 5	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 5	PHOSPHATE ION × 5 3-[(2S)-pyrrolidin-2-ylethynyl]pyridine × 5 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 9–218； UniProt 20–229 Author chain B； PDBConstruct 9–218； UniProt 20–229 Author chain C； PDBConstruct 9–218； UniProt 20–229 Author chain D； PDBConstruct 9–218； UniProt 20–229 Author chain E； PDBConstruct 9–218； UniProt 20–229 Author chain F； PDBConstruct 9–218； UniProt 20–229 Author chain G； PDBConstruct 9–218； UniProt 20–229 Author chain H； PDBConstruct 9–218； UniProt 20–229 Author chain I； PDBConstruct 9–218； UniProt 20–229 Author chain J； PDBConstruct 9–218； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4zru
Deposition date deposition_date	2015-05-12
Structure title title	X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) in complex with 3-[2-[(2S)-pyrrolidin-2-yl]ethynyl]pyridine (TI-5180)
Keywords keywords	nicotinic, acetylcholine, Ls-AChBP, ACETYLCHOLINE BINDING PROTEIN; 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.

4zru__assembly_1__model_1

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

Download this curve (.dat)

4zru__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4zru__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.39 Å
Rg (electron density)	29.63 Å
Total Rg	30.46 Å
Atom count	8190
Residues	1033
Excluded volume	142900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4zru__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4zru__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 (4)

Entity 1 Entity 1 polymer

Description description	Acetylcholine-binding protein
Molecular weight formula_weight	24859.5 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	17808

DYKDDDDKLDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSEIL

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	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	3-[(2S)-pyrrolidin-2-ylethynyl]pyridine
Molecular weight formula_weight	172.2 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1550

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d4zrua1
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	d4zrua2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4zrub1
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	d4zrub2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4zruc_
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	d4zrud1
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	d4zrud2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4zrue_
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	d4zruf1
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	d4zruf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4zrug1
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	d4zrug2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4zruh1
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	d4zruh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4zrui1
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	d4zrui2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4zruj1
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	d4zruj2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (10 domains)

Domain ID domain_id	4zruA00
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	4zruB00
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	4zruC00
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	4zruD00
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	4zruE00
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	4zruF00
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	4zruG00
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	4zruH00
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	4zruI00
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	4zruJ00
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	92.910 Å
Unit-cell length b length_b	108.870 Å
Unit-cell length c length_c	122.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.31 °
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	1.900 Å
Low-resolution limit resolution_low	90.000 Å
R factor r_factor	0.1726
R_work r_work	0.1709
R_free r_free	0.2045

X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) in complex with 3-[2-[(2S)-pyrrolidin-2-yl]ethynyl]pyridine (TI-5180)

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

4zru__assembly_1__model_1

4zru__assembly_1__model_1 | I(q)

4zru__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) 28 domains

SCOP 2.08 (18 domains)

CATH v4.4 (10 domains)

7. Citations (1)

X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) in complex with 3-[2-[(2S)-pyrrolidin-2-yl]ethynyl]pyridine (TI-5180)

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

4zru__assembly_1__model_1

4zru__assembly_1__model_1 | I(q)

4zru__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) 28 domains

SCOP 2.08 (18 domains)

CATH v4.4 (10 domains)

7. Citations (1)