3sh1

Ac-AChBP ligand binding domain mutated to human alpha-7 nAChR

Method: X-RAY DIFFRACTION Dmax: 142.4 Å Quality: GOOD

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

Soluble acetylcholine receptor

Aplysia californica

UniProt Q8WSF8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 5 其他Polymer 3 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 18–236 Chain B; UniProt 18–236 Chain C; UniProt 18–236 Chain D; UniProt 18–236 Chain E; UniProt 18–236 Fragment:unp entry 18-236 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MG MAGNESIUM ION × 4 MLK METHYLLYCACONITINE × 5 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;290 K;30%MPD, 0.1M Na Cacodylate, 0.2M Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.90 Å R-free 0.258
2 Other combination Homooligomer Protein × 5 其他Polymer 3 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 18–236 Chain G; UniProt 18–236 Chain H; UniProt 18–236 Chain I; UniProt 18–236 Chain J; UniProt 18–236 Fragment:unp entry 18-236 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 1 MLK METHYLLYCACONITINE × 5 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;290 K;30%MPD, 0.1M Na Cacodylate, 0.2M Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.90 Å R-free 0.258

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.

85 other PDB entries and 119 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8WSF8_APLCA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 10–228; UniProt 18–236 Author chain B; PDBConstruct 10–228; UniProt 18–236 Author chain C; PDBConstruct 10–228; UniProt 18–236 Author chain D; PDBConstruct 10–228; UniProt 18–236 Author chain E; PDBConstruct 10–228; UniProt 18–236 Author chain F; PDBConstruct 10–228; UniProt 18–236 Author chain G; PDBConstruct 10–228; UniProt 18–236 Author chain H; PDBConstruct 10–228; UniProt 18–236 Author chain I; PDBConstruct 10–228; UniProt 18–236 Author chain J; PDBConstruct 10–228; UniProt 18–236

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 3sh1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3sh1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3sh1
Deposition date deposition_date2011-06-15
Structure title titleAc-AChBP ligand binding domain mutated to human alpha-7 nAChR
Keywords keywordsHuman nicotinic acetylcholine receptor binding protein, Methyllycaconitine Binding, Glycosylation, RECEPTOR; RECEPTOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier43.82
Radius of gyration Rg (electron density) rg_electron43.09
Forward intensity I(0) i0991234000.00
Molecular weight molecular_weight257070.0 kDa
Excluded volume excluded_volume320150 ų
Envelope volume envelope_volume440640 ų
Hydration-shell volume shell_volume84573 ų
Envelope diameter envelope_diameter144.8
Shell Rg shell_rg49.15
Envelope Rg envelope_rg41.26
Shape Rg shape_rg43.06
Total Rg total_rg43.47
Total atoms total_atoms18107
Residues n_residues2146
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 dmax142.4
Rg (real space) rg_real43.70
Rg uncertainty (real space) rg_real_error1.10
I(0) (real space) i0_real9.9120e+08
I(0) uncertainty (real space) i0_real_error1.6700e+07
Rg (reciprocal space) rg_reciprocal43.82
I(0) (reciprocal space) i0_reciprocal991400000.0000
Solution quality estimate total_estimate0.8748
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.4
Skewness Skewness skewness0.276
Kurtosis Kurtosis kurtosis-0.364
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha115500000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.873

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd3sh1a1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sh1b1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sh1c1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1c2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sh1d1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1d2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sh1e1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1e2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sh1f1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1f2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sh1g1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1g2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sh1h1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1h2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sh1i1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1i2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sh1j1
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.96.1.0 — automated matches
Domain ID domain_idd3sh1j2
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_id3sh1A00
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_id3sh1B00
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_id3sh1C00
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_id3sh1D00
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_id3sh1E00
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_id3sh1F00
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_id3sh1G00
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_id3sh1H00
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_id3sh1I00
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_id3sh1J00
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)