3wtn

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

Method: X-RAY DIFFRACTION Dmax: 131.5 Å Quality: GOOD

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

Acetylcholine-binding protein

Lymnaea stagnalis

UniProt P58154

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 21–229 Chain B; UniProt 21–229 Chain C; UniProt 21–229 Chain D; UniProt 21–229 Chain E; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 5 CD CADMIUM ION × 35 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
10 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain H; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
11 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain I; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
12 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain J; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
2 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 21–229 Chain G; UniProt 21–229 Chain H; UniProt 21–229 Chain I; UniProt 21–229 Chain J; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 5 CD CADMIUM ION × 19 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 7 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 7 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
7 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
8 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262
9 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain G; UniProt 21–229 Fragment:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K Resolution 2.09 Å R-free 0.262

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

59 other PDB entries and 111 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3wtn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3wtn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3wtn
Deposition date deposition_date2014-04-11
Structure title titleCrystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid
Keywords keywordsneonicotinoids, nicotinic acetylcholine receptor, imidacloprid, acetylcholine binding, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.14
Radius of gyration Rg (electron density) rg_electron40.23
Forward intensity I(0) i0997456000.00
Molecular weight molecular_weight242640.0 kDa
Excluded volume excluded_volume295050 ų
Envelope volume envelope_volume387260 ų
Hydration-shell volume shell_volume78395 ų
Envelope diameter envelope_diameter134.7
Shell Rg shell_rg47.31
Envelope Rg envelope_rg38.99
Shape Rg shape_rg40.16
Total Rg total_rg40.80
Total atoms total_atoms16716
Residues n_residues2080
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax131.5
Rg (real space) rg_real40.98
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real9.9750e+08
I(0) uncertainty (real space) i0_real_error1.7330e+07
Rg (reciprocal space) rg_reciprocal41.14
I(0) (reciprocal space) i0_reciprocal997600000.0000
Solution quality estimate total_estimate0.8690
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.9
Skewness Skewness skewness0.241
Kurtosis Kurtosis kurtosis-0.300
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha143400000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.885

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd3wtna1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtna2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wtnb1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtnb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wtnc1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtnc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wtnd1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtnd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wtne1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtne2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wtnf1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtnf2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wtng1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtng2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wtnh1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtnh2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wtni1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtni2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wtnj1
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3wtnj2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (10 domains)

Domain ID domain_id3wtnA00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3wtnB00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3wtnC00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3wtnD00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3wtnE00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3wtnF00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3wtnG00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3wtnH00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3wtnI00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3wtnJ00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain

8. Citations (1)

9. Files and Curves (10)