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3u8j

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3531 (1-(pyridin-3-yl)-1,4-diazepane)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Acetylcholine-binding protein

Lymnaea stagnalis

UniProt P58154

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 5 1-(pyridin-3-yl)-1,4-diazepane × 5 SULFATE ION × 4 water × 5 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 5 1-(pyridin-3-yl)-1,4-diazepane × 5 SULFATE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3wtn 3wtn 3wtn 3wtn 3wtn 3wtn 3wtn 3wtn 3wtn 3wtn

10 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
1i9b 1i9b 1uv6 1uv6 1uw6 1uw6 1uw6 1uw6 1ux2 1ux2 2zju 2zjv

106 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
1yi5 5t90 7n0w 7n0y 7n43 7ndp 7txf

7 assemblies

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

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_id3u8j
Deposition date deposition_date2011-10-17
Structure title titleCrystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3531 (1-(pyridin-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
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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.

3u8j__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3u8j__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3u8j__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）31.17 Å
Rg (electron density)29.45 Å
Total Rg30.34 Å
Atom count8086
Residues1000
Excluded volume142310 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3u8j__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3u8j__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 (5)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd3u8ja_
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_idd3u8jb_
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_idd3u8jc_
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_idd3u8jd_
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_idd3u8je_
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_idd3u8jf_
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_idd3u8jg_
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_idd3u8jh_
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_idd3u8ji_
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_idd3u8jj_
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 (10 domains)

Domain ID domain_id3u8jA00
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_id3u8jB00
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_id3u8jC00
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_id3u8jD00
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_id3u8jE00
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_id3u8jF00
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_id3u8jG00
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_id3u8jH00
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_id3u8jI00
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_id3u8jJ00
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
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7. Citations (1)