4alx

Crystal Structure of Ls-AChBP complexed with the potent nAChR antagonist DHbE

Method: X-RAY DIFFRACTION Dmax: 131.8 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 F; UniProt 1–229 Chain G; UniProt 1–229 Chain H; UniProt 1–229 Chain I; UniProt 1–229 Chain J; UniProt 1–229 Not recorded IZN (4bS,6S)-6-methoxy-1,4,6,7,9,10,12,13-octahydro-3H,5H-pyrano[4',3':3,4]pyrido[2,1-i]indol-3-one × 5 1PE PENTAETHYLENE GLYCOL × 4 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;0.1 M HEPES PH 7.5, 25% V/V PEG 400, AND 0.2 M MGCL2. Resolution 2.30 Å R-free 0.250
2 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–229 Chain B; UniProt 1–229 Chain C; UniProt 1–229 Chain D; UniProt 1–229 Chain E; UniProt 1–229 Not recorded IZN (4bS,6S)-6-methoxy-1,4,6,7,9,10,12,13-octahydro-3H,5H-pyrano[4',3':3,4]pyrido[2,1-i]indol-3-one × 5 1PE PENTAETHYLENE GLYCOL × 2 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;0.1 M HEPES PH 7.5, 25% V/V PEG 400, AND 0.2 M MGCL2. Resolution 2.30 Å R-free 0.250

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 1–229; UniProt 1–229 Author chain B; PDBConstruct 1–229; UniProt 1–229 Author chain C; PDBConstruct 1–229; UniProt 1–229 Author chain D; PDBConstruct 1–229; UniProt 1–229 Author chain E; PDBConstruct 1–229; UniProt 1–229 Author chain F; PDBConstruct 1–229; UniProt 1–229 Author chain G; PDBConstruct 1–229; UniProt 1–229 Author chain H; PDBConstruct 1–229; UniProt 1–229 Author chain I; PDBConstruct 1–229; UniProt 1–229 Author chain J; PDBConstruct 1–229; UniProt 1–229

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 4alx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4alx
Deposition date deposition_date2012-03-06
Structure title titleCrystal Structure of Ls-AChBP complexed with the potent nAChR antagonist DHbE
Keywords keywordsACETYLCHOLINE-BINDING PROTEIN, LYMNAEA STAGNALIS, DIHYDRO-B-ERYTHROIDINE, ANTAGONIST, C-LOOP; ACETYLCHOLINE-BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.24
Radius of gyration Rg (electron density) rg_electron40.35
Forward intensity I(0) i0834095000.00
Molecular weight molecular_weight233590.0 kDa
Excluded volume excluded_volume290850 ų
Envelope volume envelope_volume387520 ų
Hydration-shell volume shell_volume78224 ų
Envelope diameter envelope_diameter141.2
Shell Rg shell_rg47.48
Envelope Rg envelope_rg39.25
Shape Rg shape_rg40.33
Total Rg total_rg40.78
Total atoms total_atoms16462
Residues n_residues2023
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 dmax131.8
Rg (real space) rg_real41.11
Rg uncertainty (real space) rg_real_error0.98
I(0) (real space) i0_real8.3410e+08
I(0) uncertainty (real space) i0_real_error1.4540e+07
Rg (reciprocal space) rg_reciprocal41.24
I(0) (reciprocal space) i0_reciprocal834200000.0000
Solution quality estimate total_estimate0.8737
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.0
Skewness Skewness skewness0.258
Kurtosis Kurtosis kurtosis-0.330
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha114500000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.881

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd4alxa_
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_idd4alxb_
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_idd4alxc_
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_idd4alxd_
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_idd4alxe_
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_idd4alxf_
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_idd4alxg_
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_idd4alxh_
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_idd4alxi_
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_idd4alxj_
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_id4alxA00
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_id4alxB00
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_id4alxC00
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_id4alxD00
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_id4alxE00
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_id4alxF00
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_id4alxG00
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_id4alxH00
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_id4alxI00
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_id4alxJ00
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)