SAXSdb — 7soh

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

Chlorotoxin

Leiurus quinquestriatus 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 1–36	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M tri-Potassium Citrate, 20% (w/v) PEG3350	Resolution 1.81 Å R-free 0.212

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 7SOH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CHL NMR SEQUENTIAL ASSIGNMENTS AND SOLUTION STRUCTURE OF CHLOROTOXIN, A SMALL SCORPION TOXIN THAT BLOCKS CHLORIDE CHANNELS Deposited 1994-11-09	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–36（36 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
5L1C Heteronuclear Solution Structure of Chlorotoxin Deposited 2016-07-28	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–36（36 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6ATW Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox Deposited 2017-08-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–36（36 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；1.1 M Na malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5 % Jeffamine ED-2001 pH 7.0	Resolution 1.53 Å R-free 0.178
7X41 Crystal structure of chlorotoxin, a glioma specific scorpion toxin Deposited 2022-03-01	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–36（36 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1 M monosodium phosphate and 0.75 M sodium citrate	Resolution 1.15 Å R-free 0.157
7X43 Crystal structure of chlorotoxin mutant - M1R Deposited 2022-03-01	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–36（36 aa）	Mutation：M1R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1 M monosodium phosphate and 0.75 M sodium citrate	Resolution 1.04 Å R-free 0.146
7X44 Crystal structure of chlorotoxin mutant - Q11N Deposited 2022-03-01	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–36（36 aa）	Mutation：Q11N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1 M monosodium phosphate and 0.75 M sodium citrate	Resolution 1.04 Å R-free 0.133
7X4D Crystal structure of chlorotoxin mutant - Y29K Deposited 2022-03-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–36（36 aa）	Mutation：Y29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1 M monosodium phosphate and 0.75 M sodium citrate	Resolution 1.55 Å R-free 0.187
8C5G Structure of human Neuropilin-1 b1b2 domains in complex with Chlorotoxin (Leiurus quinquestriatus) Deposited 2023-01-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–36（36 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.04M Potassium phosphate monobasic 16 % w/v PEG 8000 20 % v/v Glycerol (JCSG Plus: D12)	Resolution 2.70 Å R-free 0.314
8C5G Structure of human Neuropilin-1 b1b2 domains in complex with Chlorotoxin (Leiurus quinquestriatus) Deposited 2023-01-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–36（36 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.04M Potassium phosphate monobasic 16 % w/v PEG 8000 20 % v/v Glycerol (JCSG Plus: D12)	Resolution 2.70 Å R-free 0.314

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTXL_LEIQU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–38； UniProt 1–36

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7soh
Deposition date deposition_date	2021-10-30
Structure title title	Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
Keywords keywords	CDP, Chlorotoxin, 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	10.03 Å
Radius of gyration Rg (electron density) rg_electron	8.94 Å
Forward intensity I(0) i0	619119.00
Molecular weight molecular_weight	4105.0 kDa
Excluded volume excluded_volume	4741 Å³
Envelope volume envelope_volume	5443 Å³
Hydration-shell volume shell_volume	5529 Å³
Envelope diameter envelope_diameter	31.4 Å
Shell Rg shell_rg	13.85 Å
Envelope Rg envelope_rg	9.53 Å
Shape Rg shape_rg	9.03 Å
Total Rg total_rg	10.21 Å
Total atoms total_atoms	276
Residues n_residues	37
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	34.4 Å
Rg (real space) rg_real	10.02 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	6.1910e+05
I(0) uncertainty (real space) i0_real_error	6.3700e+03
Rg (reciprocal space) rg_reciprocal	10.02 Å
I(0) (reciprocal space) i0_reciprocal	619100.0000
Solution quality estimate total_estimate	0.8738
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	11.3 Å
Skewness Skewness skewness	0.350
Kurtosis Kurtosis kurtosis	-0.225
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	97550.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.982

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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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8. Citations (1)

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Unit-cell length a length_a	22.498 Å
Unit-cell length b length_b	26.350 Å
Unit-cell length c length_c	47.738 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	23.870 Å
R factor r_factor	0.1750
R_work r_work	0.1734
R_free r_free	0.2120

Description description	Chlorotoxin
Molecular weight formula_weight	4240.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	291

Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox

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

Chlorotoxin

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Leiurus quinquestriatus quinquestriatus
通用名 common_name	Egyptian scorpion, Deathstalker scorpion
NCBI Class编号 ncbi_taxonomy_id	6885
宿主生物 host_organism	Homo sapiens

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

fit	/app/data/saxs_computation/so/7soh/7soh.fit
pddf	/app/data/pr_computation/so/7soh/7soh.pr.out
profile	/app/data/saxs_computation/so/7soh/7soh.dat