3u8n

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3950 (1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane)

Method: X-RAY DIFFRACTION Dmax: 173.6 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 20–229 Chain B; UniProt 20–229 Chain C; UniProt 20–229 Chain D; UniProt 20–229 Chain E; UniProt 20–229 Not recorded 09S 1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane × 5 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;293 K;50mM Tris, 1.9 M Ammonium sulfate, 3% PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.35 Å R-free 0.230
2 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 20–229 Chain G; UniProt 20–229 Chain H; UniProt 20–229 Chain I; UniProt 20–229 Chain J; UniProt 20–229 Not recorded 09S 1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane × 5 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;293 K;50mM Tris, 1.9 M Ammonium sulfate, 3% PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.35 Å R-free 0.230
3 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain K; UniProt 20–229 Chain L; UniProt 20–229 Chain M; UniProt 20–229 Chain N; UniProt 20–229 Chain O; UniProt 20–229 Not recorded 09S 1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane × 5 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;293 K;50mM Tris, 1.9 M Ammonium sulfate, 3% PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.35 Å R-free 0.230
4 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain P; UniProt 20–229 Chain Q; UniProt 20–229 Chain R; UniProt 20–229 Chain S; UniProt 20–229 Chain T; UniProt 20–229 Not recorded 09S 1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane × 5 SO4 SULFATE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;293 K;50mM Tris, 1.9 M Ammonium sulfate, 3% PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.35 Å R-free 0.230

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 119 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 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 Author chain K; PDBConstruct 1–210; UniProt 20–229 Author chain L; PDBConstruct 1–210; UniProt 20–229 Author chain M; PDBConstruct 1–210; UniProt 20–229 Author chain N; PDBConstruct 1–210; UniProt 20–229 Author chain O; PDBConstruct 1–210; UniProt 20–229 Author chain P; PDBConstruct 1–210; UniProt 20–229 Author chain Q; PDBConstruct 1–210; UniProt 20–229 Author chain R; PDBConstruct 1–210; UniProt 20–229 Author chain S; PDBConstruct 1–210; UniProt 20–229 Author chain T; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 3u8n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3u8n
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3u8n
Deposition date deposition_date2011-10-17
Structure title titleCrystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3950 (1-(6-bromo-5-ethoxypyridin-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 methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier55.14
Radius of gyration Rg (electron density) rg_electron54.74
Forward intensity I(0) i06250200000.00
Molecular weight molecular_weight433330.0 kDa
Excluded volume excluded_volume414810 ų
Envelope volume envelope_volume806160 ų
Hydration-shell volume shell_volume117330 ų
Envelope diameter envelope_diameter180.7
Shell Rg shell_rg61.79
Envelope Rg envelope_rg53.40
Shape Rg shape_rg54.71
Total Rg total_rg54.90
Total atoms total_atoms32706
Residues n_residues4040
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 dmax173.6
Rg (real space) rg_real54.99
Rg uncertainty (real space) rg_real_error1.42
I(0) (real space) i0_real6.2500e+09
I(0) uncertainty (real space) i0_real_error1.2580e+08
Rg (reciprocal space) rg_reciprocal55.24
I(0) (reciprocal space) i0_reciprocal6252000000.0000
Solution quality estimate total_estimate0.8768
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary59.9
Skewness Skewness skewness0.194
Kurtosis Kurtosis kurtosis-0.623
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha645800000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.615

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd3u8na_
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_idd3u8nb_
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_idd3u8nc_
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_idd3u8nd_
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_idd3u8ne_
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_idd3u8nf_
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_idd3u8ng_
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_idd3u8nh_
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_idd3u8ni_
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_idd3u8nj_
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_idd3u8nk_
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_idd3u8nl_
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_idd3u8nm_
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_idd3u8nn_
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_idd3u8no_
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_idd3u8np_
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_idd3u8nq_
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_idd3u8nr_
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_idd3u8ns_
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_idd3u8nt_
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

CATH v4.4 (20 domains)

Domain ID domain_id3u8nA00
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_id3u8nB00
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_id3u8nC00
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_id3u8nD00
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_id3u8nE00
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_id3u8nF00
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_id3u8nG00
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_id3u8nH00
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_id3u8nI00
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_id3u8nJ00
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_id3u8nK00
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_id3u8nL00
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_id3u8nM00
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_id3u8nN00
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_id3u8nO00
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_id3u8nP00
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_id3u8nQ00
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_id3u8nR00
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_id3u8nS00
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_id3u8nT00
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)