7ndp

X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001856.

Method: X-RAY DIFFRACTION Dmax: 126.2 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 Other combination Homooligomer Protein × 5 其他Polymer 1 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 5 U8T 6-bromanylspiro[3~{H}-chromene-2,4'-piperidine]-4-one × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;PEG3350 3% Ammonium sulphate 1.8M HEPES buffer 0.1M, pH 7.75 Resolution 2.00 Å R-free 0.243
2 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 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 U8T 6-bromanylspiro[3~{H}-chromene-2,4'-piperidine]-4-one × 4 SO4 SULFATE ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;PEG3350 3% Ammonium sulphate 1.8M HEPES buffer 0.1M, pH 7.75 Resolution 2.00 Å R-free 0.243

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 7ndp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ndp
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id7ndp
Deposition date deposition_date2021-02-02
Structure title titleX-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001856.
Keywords keywordsFragment based drug design, Acetylcholine-binding protein, CHOLINE-BINDING PROTEIN; CHOLINE-BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.17
Radius of gyration Rg (electron density) rg_electron40.29
Forward intensity I(0) i0850395000.00
Molecular weight molecular_weight233490.0 kDa
Excluded volume excluded_volume289670 ų
Envelope volume envelope_volume391040 ų
Hydration-shell volume shell_volume79027 ų
Envelope diameter envelope_diameter135.6
Shell Rg shell_rg47.55
Envelope Rg envelope_rg39.01
Shape Rg shape_rg40.26
Total Rg total_rg40.76
Total atoms total_atoms16416
Residues n_residues2019
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 dmax126.2
Rg (real space) rg_real41.02
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real8.5040e+08
I(0) uncertainty (real space) i0_real_error1.3020e+07
Rg (reciprocal space) rg_reciprocal41.16
I(0) (reciprocal space) i0_reciprocal850500000.0000
Solution quality estimate total_estimate0.8635
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.1
Skewness Skewness skewness0.244
Kurtosis Kurtosis kurtosis-0.342
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha136700000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.569

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd7ndpa_
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_idd7ndpb_
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_idd7ndpc_
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_idd7ndpd_
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_idd7ndpe_
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_idd7ndpf_
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_idd7ndpg_
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_idd7ndph_
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_idd7ndpi_
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_idd7ndpj_
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

8. Citations (1)

9. Files and Curves (10)