SAXSdb — 2atb

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

neurotoxin alpha-IT

Leiurus quinquestriatus

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 20–82	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 20–82	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

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 2ATB	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 mutation/modification 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 mutation/modification 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
2YEO A39L mutation of scorpion toxin lqh-alpha-it Deposited 2011-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 20–83（64 aa） 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
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 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 5 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 20–82 Author chain B； PDBConstruct 2–65； UniProt 20–82

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2atb
Deposition date deposition_date	2005-08-24
Structure title title	Triple mutant 8D9D10V of scorpion toxin LQH-alpha-IT
Keywords keywords	alpha toxin, muation, scorpion, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	17.31 Å
Radius of gyration Rg (electron density) rg_electron	16.78 Å
Forward intensity I(0) i0	4977570.00
Molecular weight molecular_weight	14908.0 kDa
Excluded volume excluded_volume	18039 Å³
Envelope volume envelope_volume	21170 Å³
Hydration-shell volume shell_volume	11483 Å³
Envelope diameter envelope_diameter	57.2 Å
Shell Rg shell_rg	21.16 Å
Envelope Rg envelope_rg	17.01 Å
Shape Rg shape_rg	16.77 Å
Total Rg total_rg	17.56 Å
Total atoms total_atoms	1033
Residues n_residues	130
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	59.4 Å
Rg (real space) rg_real	17.40 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	4.9780e+06
I(0) uncertainty (real space) i0_real_error	6.0670e+04
Rg (reciprocal space) rg_reciprocal	17.39 Å
I(0) (reciprocal space) i0_reciprocal	4978000.0000
Solution quality estimate total_estimate	0.7062
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.0 Å
Skewness Skewness skewness	0.419
Kurtosis Kurtosis kurtosis	-0.431
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	587300.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 0.307; Positv: 1.000; Valcen: 0.785; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	neurotoxin alpha-IT
Molecular weight formula_weight	7319.3 kDa
Mutation mutation	K9D, N10D, Y11V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1253

MVRDAYIADDVNCVYECFRDAYCNELCTKNGASSGYCQWAGKYGNACWCYALPDNVPIRVPGKCR

来源 Source

来源生物 organism	Leiurus quinquestriatus
通用名 common_name	Egyptian scorpion
NCBI Class编号 ncbi_taxonomy_id	6883
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2atba_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.7 — Scorpion toxin-like
Family Family family	g.3.7.1 — Long-chain scorpion toxins

Domain ID domain_id	d2atbb_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.7 — Scorpion toxin-like
Family Family family	g.3.7.1 — Long-chain scorpion toxins

CATH v4.4 (2 domains)

Domain ID domain_id	2atbA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	10 — Knottin, scorpion toxin-like

Domain ID domain_id	2atbB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	10 — Knottin, scorpion toxin-like

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8. Citations (1)

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Unit-cell length a length_a	70.907 Å
Unit-cell length b length_b	70.907 Å
Unit-cell length c length_c	170.681 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1290
R_work r_work	0.1270
R_free r_free	0.1700

fit	/app/data/saxs_computation/at/2atb/2atb.fit
pddf	/app/data/pr_computation/at/2atb/2atb.pr.out
profile	/app/data/saxs_computation/at/2atb/2atb.dat

Triple mutant 8D9D10V of scorpion toxin LQH-alpha-IT

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

neurotoxin alpha-IT

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction