4zjt

X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (LsAChBP) in complex with 2-Thiophenylmethylene Anabaseine (2TAB)

Method: X-RAY DIFFRACTION Dmax: 138.2 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 Fragment:UNP residues 20-229 PO4 PHOSPHATE ION × 5 4P6 (3E)-3-(thiophen-2-ylmethylidene)-3,4,5,6-tetrahydro-2,3'-bipyridine × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.26 M ammonium phosphate, 35% glycerol Resolution 1.85 Å R-free 0.225
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 Fragment:UNP residues 20-229 PO4 PHOSPHATE ION × 5 4P6 (3E)-3-(thiophen-2-ylmethylidene)-3,4,5,6-tetrahydro-2,3'-bipyridine × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.26 M ammonium phosphate, 35% glycerol Resolution 1.85 Å R-free 0.225

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 121 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 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.

SAXS scattering curve SAXS Profile

SAXS profile for 4zjt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zjt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4zjt
Deposition date deposition_date2015-04-29
Structure title titleX-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (LsAChBP) in complex with 2-Thiophenylmethylene Anabaseine (2TAB)
Keywords keywordsnicotinic, AChBP, receptor, Anabaseine, ACETYLCHOLINE BINDING PROTEIN; ACETYLCHOLINE BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.75
Radius of gyration Rg (electron density) rg_electron41.00
Forward intensity I(0) i0895786000.00
Molecular weight molecular_weight238060.0 kDa
Excluded volume excluded_volume294270 ų
Envelope volume envelope_volume396960 ų
Hydration-shell volume shell_volume78848 ų
Envelope diameter envelope_diameter152.4
Shell Rg shell_rg47.79
Envelope Rg envelope_rg40.09
Shape Rg shape_rg40.98
Total Rg total_rg41.42
Total atoms total_atoms16910
Residues n_residues2115
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 dmax138.2
Rg (real space) rg_real41.61
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real8.9580e+08
I(0) uncertainty (real space) i0_real_error1.4920e+07
Rg (reciprocal space) rg_reciprocal41.75
I(0) (reciprocal space) i0_reciprocal895900000.0000
Solution quality estimate total_estimate0.8659
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.9
Skewness Skewness skewness0.263
Kurtosis Kurtosis kurtosis-0.294
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha93450000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.964

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd4zjta1
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_idd4zjta2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjtb1
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_idd4zjtb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjtc1
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_idd4zjtc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjtd1
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_idd4zjtd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjte1
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_idd4zjte2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjtf1
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_idd4zjtf2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjtg1
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_idd4zjtg2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjth1
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_idd4zjth2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjti1
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_idd4zjti2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjtj1
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_idd4zjtj2
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_id4zjtA00
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_id4zjtB00
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_id4zjtC00
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_id4zjtD00
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_id4zjtE00
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_id4zjtF00
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_id4zjtG00
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_id4zjtH00
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_id4zjtI00
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_id4zjtJ00
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)