5tvc

Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine (TI-5312)

Method: X-RAY DIFFRACTION Dmax: 89.8 Å Quality: EXCELLENT

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

Soluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera

Homo sapiens

UniProt P32297

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 215–230 Chain B; UniProt 215–230 Chain C; UniProt 215–230 Chain D; UniProt 215–230 Chain E; UniProt 215–230 Fragment:UNP residues 18-198 + 215-236 from Aplysia californica linked by loop C (UNP residues 215-230) from Homo sapiens SO4 SULFATE ION × 6 1PE PENTAETHYLENE GLYCOL × 1 7LB (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;313 K;1.7% PEG 400, 0.085 M HEPES - Na pH 7.5, 1.7 M Ammonium Sulfate, 15% Glycerol Resolution 1.93 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.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACHA3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 191–206; UniProt 215–230 Author chain B; PDBConstruct 191–206; UniProt 215–230 Author chain C; PDBConstruct 191–206; UniProt 215–230 Author chain D; PDBConstruct 191–206; UniProt 215–230 Author chain E; PDBConstruct 191–206; UniProt 215–230

Soluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera

Homo sapiens

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 Insufficient information Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 18–198 Chain A; UniProt 215–236 Chain B; UniProt 18–198 Chain B; UniProt 215–236 Chain C; UniProt 18–198 Chain C; UniProt 215–236 Chain D; UniProt 18–198 Chain D; UniProt 215–236 Chain E; UniProt 18–198 Chain E; UniProt 215–236 Fragment:UNP residues 18-198 + 215-236 from Aplysia californica linked by loop C (UNP residues 215-230) from Homo sapiens SO4 SULFATE ION × 6 1PE PENTAETHYLENE GLYCOL × 1 7LB (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;313 K;1.7% PEG 400, 0.085 M HEPES - Na pH 7.5, 1.7 M Ammonium Sulfate, 15% Glycerol Resolution 1.93 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.

85 other PDB entries and 120 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 10–190; UniProt 18–198 Author chain A; PDBConstruct 207–228; UniProt 215–236 Author chain B; PDBConstruct 10–190; UniProt 18–198 Author chain B; PDBConstruct 207–228; UniProt 215–236 Author chain C; PDBConstruct 10–190; UniProt 18–198 Author chain C; PDBConstruct 207–228; UniProt 215–236 Author chain D; PDBConstruct 10–190; UniProt 18–198 Author chain D; PDBConstruct 207–228; UniProt 215–236 Author chain E; PDBConstruct 10–190; UniProt 18–198 Author chain E; PDBConstruct 207–228; UniProt 215–236

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 5tvc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tvc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tvc
Deposition date deposition_date2016-11-08
Structure title titleCrystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine (TI-5312)
Keywords keywordsnicotinic, acetylcholine, AChBP, chimeric protein, 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_guinier31.49
Radius of gyration Rg (electron density) rg_electron29.89
Forward intensity I(0) i0206797000.00
Molecular weight molecular_weight113370.0 kDa
Excluded volume excluded_volume141190 ų
Envelope volume envelope_volume180770 ų
Hydration-shell volume shell_volume48011 ų
Envelope diameter envelope_diameter93.0
Shell Rg shell_rg39.09
Envelope Rg envelope_rg29.18
Shape Rg shape_rg29.90
Total Rg total_rg30.71
Total atoms total_atoms7993
Residues n_residues1020
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 dmax89.8
Rg (real space) rg_real31.17
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real2.0680e+08
I(0) uncertainty (real space) i0_real_error2.5290e+06
Rg (reciprocal space) rg_reciprocal31.31
I(0) (reciprocal space) i0_reciprocal206800000.0000
Solution quality estimate total_estimate0.9048
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.9
Skewness Skewness skewness-0.078
Kurtosis Kurtosis kurtosis-0.611
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41970000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.928

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5tvca1
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_idd5tvca2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5tvcb_
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_idd5tvcc1
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_idd5tvcc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5tvcd_
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_idd5tvce1
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_idd5tvce2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (5 domains)

Domain ID domain_id5tvcA00
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_id5tvcB00
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_id5tvcC00
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_id5tvcD00
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_id5tvcE00
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)