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9baf

Solution NMR structure of conofurin-Delta

Method: SOLUTION NMR Dmax: 23.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-conotoxin LvIA

OrganismNot specified

UniProt L8BU87

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 21–36 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 2.5；288 K；Ionic strength (raw mmCIF value) nd；Pressure 1 NMR sample composition：2.0 mg/mL peptide, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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.

Other PDB Difference from Current Entry 9BAF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MDQ A Novel 4/7-Conotoxin LvIA from Conus lividus that Selectively Blocks 3 2 vs. 6/3 2 3 Nicotinic Acetylcholine Receptors Deposited 2013-09-16 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–36（16 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4；Pressure ambient
NMR measurement conditions pH 4；298 K；Pressure ambient
NMR sample composition 1.5 mM H2O, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.5 mM D2O, 100% D2O | 100% D2O
Resolution not provided
5XGL Co-crystal structure of Ac-AChBPP in complex with alpha-conotoxin LvIA Deposited 2017-04-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 21–36（16 aa）
Chain E 21–36（16 aa）
Chain F 21–36（16 aa）
Chain H 21–36（16 aa）
Chain J 21–36（16 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1M Bis-Tris propane PH 7.0
Resolution 3.44 Å R-free 0.283
6M4X Co-crystal structure of Ac-AChBPP in complex with [N9A]LvIA Deposited 2020-03-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 21–36（16 aa）
Chain E 21–36（16 aa）
Chain F 21–36（16 aa）
Chain H 21–36（16 aa）
Chain J 21–36（16 aa）
Mutation：N29A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N29A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N29A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N29A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N29A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M Magnesium sulfate hydrate, 0.1 M Sodium acetate trihydrate (pH 4.6)
Resolution 3.00 Å R-free 0.316
6M4Z Co-crystal structure of Ac-AChBPP in complex with alpha-conotoxin [D11A]LvIA Deposited 2020-03-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 21–36（16 aa）
Chain E 21–36（16 aa）
Chain F 21–36（16 aa）
Chain H 21–36（16 aa）
Chain J 21–36（16 aa）
Mutation：D31A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D31A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D31A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D31A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D31A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.2 M Sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane (pH 7.0)
Resolution 2.80 Å R-free 0.268

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

View Construct and Data Evidence
UniProt name CA1A_CONLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–16； UniProt 21–36

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 9baf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9baf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9baf
Deposition date deposition_date2024-04-04
Structure title titleSolution NMR structure of conofurin-Delta
Keywords keywordsconotoxin, nicotinic acetylcholine receptor, NEUROPEPTIDE; NEUROPEPTIDE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier6.61 Å
Radius of gyration Rg (electron density) rg_electron6.72 Å
Forward intensity I(0) i031276600.00
Molecular weight molecular_weight35062.0 kDa
Excluded volume excluded_volume39649 ų
Envelope volume envelope_volume4611 ų
Hydration-shell volume shell_volume5090 ų
Envelope diameter envelope_diameter26.0 Å
Shell Rg shell_rg13.11 Å
Envelope Rg envelope_rg8.77 Å
Shape Rg shape_rg6.72 Å
Total Rg total_rg6.99 Å
Total atoms total_atoms4640
Residues n_residues320
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax23.8 Å
Rg (real space) rg_real6.63 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real3.1280e+07
I(0) uncertainty (real space) i0_real_error2.8330e+05
Rg (reciprocal space) rg_reciprocal6.64 Å
I(0) (reciprocal space) i0_reciprocal31280000.0000
Solution quality estimate total_estimate0.8329
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary7.8 Å
Skewness Skewness skewness0.492
Kurtosis Kurtosis kurtosis0.118
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1861.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.724; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.840; Smooth: 0.813
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)