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1ptx

CRYSTAL STRUCTURE OF TOXIN II FROM THE SCORPION ANDROCTONUS AUSTRALIS HECTOR REFINED AT 1.3 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 37.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SCORPION TOXIN II

Androctonus australis

UniProt P01484

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 20–83 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.30 Å

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 1PTX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AHO THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPION PROTEIN TOXIN Deposited 1997-04-08 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–83（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；pH 6.8
Resolution 0.96 Å
1SEG Crystal structure of a toxin chimera between Lqh-alpha-IT from the scorpion Leiurus quinquestriatus hebraeus and AAH2 from Androctonus australis hector Deposited 2004-02-17 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–83（64 aa）
Mutation：D8K, D9N, V10Y, G17F, R56P, T57I, K58R, G59V, R62K SO4 SULFATE ION × 1 NO3 NITRATE ION × 2 PPI PROPANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；296 K；100mM trisodium citrate dihydrate, 1M mono-ammonium dihydrogen phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.30 Å R-free 0.178
4AEI Crystal structure of the AaHII-Fab4C1 complex Deposited 2012-01-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 20–83（64 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；15% PEG 2000 MME, 0.1 M HEPES PH 8.0, 0.1 M NACL
Resolution 2.30 Å R-free 0.254
4AEI Crystal structure of the AaHII-Fab4C1 complex Deposited 2012-01-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 20–83（64 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；15% PEG 2000 MME, 0.1 M HEPES PH 8.0, 0.1 M NACL
Resolution 2.30 Å R-free 0.254
4AEI Crystal structure of the AaHII-Fab4C1 complex Deposited 2012-01-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 20–83（64 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；15% PEG 2000 MME, 0.1 M HEPES PH 8.0, 0.1 M NACL
Resolution 2.30 Å R-free 0.254
6NT4 Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2. Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 20–83（64 aa）
Chain C 20–83（64 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 76F (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate × 5 AJP Digitonin × 1 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

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

View Construct and Data Evidence
UniProt name SCX2_ANDAU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–64； 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 1ptx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ptx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ptx
Deposition date deposition_date1994-09-02
Structure title titleCRYSTAL STRUCTURE OF TOXIN II FROM THE SCORPION ANDROCTONUS AUSTRALIS HECTOR REFINED AT 1.3 ANGSTROMS RESOLUTION
Keywords keywordsTOXIN; 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_guinier12.02 Å
Radius of gyration Rg (electron density) rg_electron10.86 Å
Forward intensity I(0) i01362830.00
Molecular weight molecular_weight7253.0 kDa
Excluded volume excluded_volume8798 ų
Envelope volume envelope_volume9681 ų
Hydration-shell volume shell_volume7857 ų
Envelope diameter envelope_diameter36.5 Å
Shell Rg shell_rg16.12 Å
Envelope Rg envelope_rg11.20 Å
Shape Rg shape_rg10.87 Å
Total Rg total_rg12.17 Å
Total atoms total_atoms505
Residues n_residues64
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 dmax37.9 Å
Rg (real space) rg_real11.95 Å
Rg uncertainty (real space) rg_real_error0.19 Å
I(0) (real space) i0_real1.3630e+06
I(0) uncertainty (real space) i0_real_error1.2400e+04
Rg (reciprocal space) rg_reciprocal11.96 Å
I(0) (reciprocal space) i0_reciprocal1363000.0000
Solution quality estimate total_estimate0.9031
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.9 Å
Skewness Skewness skewness0.150
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha187800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.967
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ptxa_
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

CATH v4.4 (1 domains)

Domain ID domain_id1ptxA00
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 (4)

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9. Files and Curves (10)