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2yeo

A39L mutation of scorpion toxin lqh-alpha-it

Method: X-RAY DIFFRACTION Dmax: 40.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ALPHA-INSECT TOXIN LQHAIT

LEIURUS QUINQUESTRIATUS HEBRAEUS

UniProt P17728

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 20–83 Fragment：RESIDUES 20-83 Mutation：YES DR8 N,N,N-TRIMETHYLHEPTA-1,3,5-TRIYN-1-AMINIUM × 3 DR0 N-(HYDROXYMETHYL)-N,N-DIMETHYLHEXAN-1-AMINIUM × 3 EDO 1,2-ETHANEDIOL × 12 CL CHLORIDE ION × 9 X-RAY DIFFRACTION X-ray crystallization conditions：0.01 M HEXADECYLTRIMETHYLAMMONIUM BROMIDE, 0.5 M SODIUM CHLORIDE, 0.01 M MAGNESIUM CHLORIDE HEXAHYDRATE PROTEIN MOLECULE WAS OF 10MG/ML DISSOLVED IN DISTILLED WATER Resolution 1.08 Å R-free 0.123

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 2YEO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1LQH INSECTICIDAL ALPHA SCORPION TOXIN ISOLATED FROM THE VENOM OF SCORPION LEIURUS QUINQUESTRIATUS HEBRAEUS, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–82（63 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1LQI INSECTICIDAL ALPHA SCORPION TOXIN ISOLATED FROM THE VENOM OF SCORPION LEIURUS QUINQUESTRIATUS HEBRAEUS, NMR, 29 STRUCTURES Deposited 1996-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–82（63 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2ATB Triple mutant 8D9D10V of scorpion toxin LQH-alpha-IT Deposited 2005-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–82（63 aa）
Mutation：K9D, N10D, Y11V NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.01M Cobaltous Chlorid hexahydrate, 0.1M Sodium Acetate trihydrate, 1M of 1,6 Hexnediol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.60 Å R-free 0.170
2ATB Triple mutant 8D9D10V of scorpion toxin LQH-alpha-IT Deposited 2005-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 20–82（63 aa）
Mutation：K9D, N10D, Y11V NO3 NITRATE ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.01M Cobaltous Chlorid hexahydrate, 0.1M Sodium Acetate trihydrate, 1M of 1,6 Hexnediol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.60 Å R-free 0.170
8VQC Structure of the voltage-gated sodium channel NavPas from American Cockroach Periplaneta Americana in complex with scorpion alpha-toxin LqhaIT Deposited 2024-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 20–82（63 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM Tris pH 7.5, 50 mM NaCl, 0.1% (w/v) digitonin
cryo-EM vitrification conditions Cryogen ETHANE；Sample was applied on the grid in Vitrobot Mark IV chamber (Thermo Fisher Scientific), blotted for 4 secs with a blot force of 25 and then plunged into ethane
Resolution 3.90 Å
9LKZ Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and scorpion alpha toxin LqhaIT Deposited 2025-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 20–85（66 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SCXA_LEIQH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–65； UniProt 20–83

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 2yeo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2yeo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2yeo
Deposition date deposition_date2011-03-28
Structure title titleA39L mutation of scorpion toxin lqh-alpha-it
Keywords keywordsTOXIN, DEFENSE RESPONSE; TOXIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.31 Å
Radius of gyration Rg (electron density) rg_electron11.38 Å
Forward intensity I(0) i01508540.00
Molecular weight molecular_weight8033.0 kDa
Excluded volume excluded_volume9931 ų
Envelope volume envelope_volume10841 ų
Hydration-shell volume shell_volume8374 ų
Envelope diameter envelope_diameter38.5 Å
Shell Rg shell_rg16.69 Å
Envelope Rg envelope_rg11.89 Å
Shape Rg shape_rg11.34 Å
Total Rg total_rg12.81 Å
Total atoms total_atoms1081
Residues n_residues65
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 dmax40.7 Å
Rg (real space) rg_real12.26 Å
Rg uncertainty (real space) rg_real_error0.29 Å
I(0) (real space) i0_real1.5090e+06
I(0) uncertainty (real space) i0_real_error1.8050e+04
Rg (reciprocal space) rg_reciprocal12.26 Å
I(0) (reciprocal space) i0_reciprocal1509000.0000
Solution quality estimate total_estimate0.8900
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.0 Å
Skewness Skewness skewness0.206
Kurtosis Kurtosis kurtosis-0.321
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha196400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.861; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2yeoa1
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.7 — Scorpion toxin-like
Family Family familyg.3.7.1 — Long-chain scorpion toxins
Domain ID domain_idd2yeoa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2yeoA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology30 — Defensin A-like
Homologous superfamily homologous superfamily10 — Knottin, scorpion toxin-like
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8. Citations (1)

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9. Files and Curves (10)