3wtn

Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid

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	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 5 CADMIUM ION × 35 SODIUM ION × 2 water × 5	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 2 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 6 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 2 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 5	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 5 CADMIUM ION × 19 water × 5	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 8 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 7 SODIUM ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 7 SODIUM ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 7 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 6 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 4 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CADMIUM ION × 5 water × 1	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 6–214； UniProt 21–229 Author chain B； PDBConstruct 6–214； UniProt 21–229 Author chain C； PDBConstruct 6–214； UniProt 21–229 Author chain D； PDBConstruct 6–214； UniProt 21–229 Author chain E； PDBConstruct 6–214； UniProt 21–229 Author chain F； PDBConstruct 6–214； UniProt 21–229 Author chain G； PDBConstruct 6–214； UniProt 21–229 Author chain H； PDBConstruct 6–214； UniProt 21–229 Author chain I； PDBConstruct 6–214； UniProt 21–229 Author chain J； PDBConstruct 6–214； UniProt 21–229

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	3wtn
Deposition date deposition_date	2014-04-11
Structure title title	Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid
Keywords keywords	neonicotinoids, nicotinic acetylcholine receptor, imidacloprid, acetylcholine binding, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

3wtn__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3wtn__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wtn__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	21.04 Å
Rg (electron density)	19.47 Å
Total Rg	21.00 Å
Atom count	1674
Residues	208
Excluded volume	29614 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wtn__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3wtn__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3wtn__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3wtn__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3wtn__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3wtn__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3wtn__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3wtn__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3wtn__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3wtn__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3wtn__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3wtn__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Acetylcholine-binding protein
Molecular weight formula_weight	24221.8 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	18230

EAEAADRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWDSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSEIL

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	Pichia pastoris

Entity 2 Entity 2 non-polymer

Description description	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine
Molecular weight formula_weight	210.7 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	54

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1336

▼

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d3wtna1
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	d3wtna2
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	d3wtnb1
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	d3wtnb2
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	d3wtnc1
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	d3wtnc2
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	d3wtnd1
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	d3wtnd2
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	d3wtne1
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	d3wtne2
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	d3wtnf1
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	d3wtnf2
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	d3wtng1
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	d3wtng2
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	d3wtnh1
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	d3wtnh2
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	d3wtni1
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	d3wtni2
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	d3wtnj1
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	d3wtnj2
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	3wtnA00
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	3wtnB00
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	3wtnC00
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	3wtnD00
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	3wtnE00
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	3wtnF00
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	3wtnG00
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	3wtnH00
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	3wtnI00
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	3wtnJ00
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	77.006 Å
Unit-cell length b length_b	118.401 Å
Unit-cell length c length_c	243.591 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	40

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	47.840 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2620

Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid

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

3wtn__assembly_5__model_1

3wtn__assembly_5__model_1 | I(q)

3wtn__assembly_5__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid

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

3wtn__assembly_5__model_1

3wtn__assembly_5__model_1 | I(q)

3wtn__assembly_5__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

CATH v4.4 (10 domains)

7. Citations (1)