SAXSdb — 5i5b

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

Kappa-stichotoxin-She3a

OrganismNot specified

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–35	Non-standard monomer：Yes (specific site not provided by mmCIF)	D-ShK × 1 SO4 SULFATE ION × 4 LI LITHIUM ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350 NaCl	Resolution 0.90 Å R-free 0.128

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 5I5B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BEI Shk-dnp22: A Potent Kv1.3-specific immunosuppressive polypeptide, NMR, 20 structures Deposited 1998-05-14	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 1–35（35 aa）	Mutation：K22DNP, DIAMINOPROPANOATE (DNP) SUBSTITUTION AT POSITION 22 Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.9；293 K NMR sample composition 10% D2O OR 100% D2O	Resolution not provided
1C2U SOLUTION STRUCTURE OF [ABU3,35]SHK12-28,17-32 Deposited 1999-07-27	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 1–35（35 aa）	Mutation：C3(ABU), C35(ABU), M21A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；293 K；Ionic strength (raw mmCIF value) 5.6 mM PEPTIDE；Pressure AMBIENT NMR sample composition 5.6 MM [ABU3,35]SHK12-28,17-32; 90% H2O, 10% D2O (V/V)	Resolution not provided
1ROO NMR SOLUTION STRUCTURE OF SHK TOXIN, NMR, 20 STRUCTURES Deposited 1996-01-11	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 1–35（35 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；293 K	Resolution not provided
2K9E NMR Solution Structure for ShK-192: A Potent KV1.3-Specific Immunosuppressive Polypeptide Deposited 2008-10-09	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 1–35（35 aa）	Mutation：M21(NLE) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.79；293 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR measurement conditions pH 4.1；278 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition 3.0 mM ShK-192, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3.0 mM ShK-192, 100% D2O \| 100% D2O	Resolution not provided
4LFQ High resolution x-ray crystal structure of L-ShK toxin Deposited 2013-06-27	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 1–35（35 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；2.1 M DL-Malic acid, pH 7, vapor diffusion, hanging drop, temperature 292K	Resolution 1.06 Å R-free 0.160
4LFS High resolution x-ray structure of racemic ShK toxin Deposited 2013-06-27	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 1–35（35 aa）	Not recorded	CL CHLORIDE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；0.2 M Lithium sulfate monohydrate, 0.1 M Tris, pH 8.5, 25 % Polyethylene glycol 3,350, 20 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 0.97 Å R-free 0.158
4Z7P X-ray structure of racemic ShK Q16K toxin Deposited 2015-04-07	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 1–35（35 aa）	Mutation：Q16K	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M sodium acetate pH 4.5, 2-2.5 M ammonium sulfate	Resolution 1.20 Å R-free 0.227
5I5A quasi racemic structure of allo-Ile7-ShK and D-ShK Deposited 2016-02-14	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 1–35（35 aa）	Not recorded	GOL GLYCEROL × 2 NA SODIUM ION × 1 LI LITHIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；2.1 M D/L-Malic acid NaCl	Resolution 1.20 Å R-free 0.195
5I5A quasi racemic structure of allo-Ile7-ShK and D-ShK Deposited 2016-02-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–35（35 aa）	Not recorded	GOL GLYCEROL × 4 NA SODIUM ION × 2 LI LITHIUM ION × 2 MLT D-MALATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；2.1 M D/L-Malic acid NaCl	Resolution 1.20 Å R-free 0.195
5I5C X-ray crystal structure of allo-Thr31-ShK Deposited 2016-02-15	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 1–35（35 aa） Chain B 1–35（35 aa） Chain C 1–35（35 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)	SO4 SULFATE ION × 4 LI LITHIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS 25% w/v Polyethylene glycol 3,350	Resolution 1.30 Å R-free 0.169

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	K1A_STIHL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–35； UniProt 1–35

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	5i5b
Deposition date deposition_date	2016-02-15
Structure title title	quasi racemic structure of allo-Thr13-ShK and D-ShK
Keywords keywords	allo-Thr13-ShK, D-ShK, quasi racemic structure, 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	13.71 Å
Radius of gyration Rg (electron density) rg_electron	13.00 Å
Forward intensity I(0) i0	1965260.00
Molecular weight molecular_weight	8672.0 kDa
Excluded volume excluded_volume	10542 Å³
Envelope volume envelope_volume	12527 Å³
Hydration-shell volume shell_volume	8725 Å³
Envelope diameter envelope_diameter	47.0 Å
Shell Rg shell_rg	17.70 Å
Envelope Rg envelope_rg	13.31 Å
Shape Rg shape_rg	13.02 Å
Total Rg total_rg	14.04 Å
Total atoms total_atoms	586
Residues n_residues	35
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	47.0 Å
Rg (real space) rg_real	13.76 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.9650e+06
I(0) uncertainty (real space) i0_real_error	2.3690e+04
Rg (reciprocal space) rg_reciprocal	13.76 Å
I(0) (reciprocal space) i0_reciprocal	1965000.0000
Solution quality estimate total_estimate	0.7871
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.3 Å
Skewness Skewness skewness	0.456
Kurtosis Kurtosis kurtosis	-0.198
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	481800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.789; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Kappa-stichotoxin-She3a
Molecular weight formula_weight	4069.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	756

RSCIDTIPKSRCTAFQCKHSMKYRLSFCRKTCGTC

Entity 2 Entity 2 polymer

Description description	D-ShK
Molecular weight formula_weight	4065.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(D)
Chain IDs strand_id	B

RSCIDTIPKSRCTAFQCKHSMKYRLSFCRKTCGTC

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	LITHIUM ION
Molecular weight formula_weight	6.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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8. Citations (1)

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Unit-cell length a length_a	21.457 Å
Unit-cell length b length_b	24.935 Å
Unit-cell length c length_c	29.935 Å
Unit-cell angle α angle_alpha	113.82 °
Unit-cell angle β angle_beta	90.42 °
Unit-cell angle γ angle_gamma	98.98 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	0.900 Å
Low-resolution limit resolution_low	27.300 Å
R factor r_factor	0.1132
R_work r_work	0.1125
R_free r_free	0.1275

fit	/app/data/saxs_computation/i5/5i5b/5i5b.fit
pddf	/app/data/pr_computation/i5/5i5b/5i5b.pr.out
profile	/app/data/saxs_computation/i5/5i5b/5i5b.dat

quasi racemic structure of allo-Thr13-ShK and D-ShK

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

Kappa-stichotoxin-She3a

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)