SAXSdb — 8v68

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

Saxiphilin

Nanorana parkeri

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 1–854	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 YGF (3aS,4R,7R,10aS)-2,6-diamino-4-(hydroxymethyl)-3a,4,8,9-tetrahydro-1H,10H-pyrrolo[1,2-c]purine-10,10-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；277.15 K；20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0, dcSTX:NpSxph molar ratio 1.2:1	Resolution 1.90 Å R-free 0.225

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 8V68	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8V65 Nanorana parkeri saxiphilin:dcGTX2 (co-crystal) Deposited 2023-12-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–854（854 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 YGU (3aS,4R,7R,9R,10aS)-2,6-diamino-10,10-dihydroxy-4-(hydroxymethyl)-3a,4,9,10-tetrahydro-1H,8H-pyrrolo[1,2-c]purin-9-yl hydrogen sulfate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277.15 K；20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0, dcGTX2&3:NpSxph molar ratio 1.2:1	Resolution 1.80 Å R-free 0.218
8V66 Nanorana parkeri saxiphilin:GTX5 (co-crystal) Deposited 2023-12-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–854（854 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 YGZ ({[(3aS,4R,7S,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methoxy}carbonyl)sulfamic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277.15 K；20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0, GTX5:NpSxph molar ratio 1.2:1	Resolution 1.90 Å R-free 0.218
8V67 Nanorana parkeri saxiphilin:C1 (co-crystal) Deposited 2023-12-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–854（854 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 YH9 ({[(3aS,4R,7R,9R,10aS)-2,6-diamino-10,10-dihydroxy-9-(sulfooxy)-3a,4,9,10-tetrahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methoxy}carbonyl)sulfamic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277.15 K；20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0, C1&C2:NpSxph molar ratio 1.2:1	Resolution 1.90 Å R-free 0.229
8V69 Nanorana parkeri saxiphilin:GTX2 (co-crystal) Deposited 2023-12-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–854（854 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 YGQ Gonyautoxin II × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277.15 K；20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0, GTX2&3:NpSxph molar ratio 1.2:1	Resolution 1.95 Å R-free 0.212
9Y91 Nanorana parkeri saxiphilin:STX-C13-NBz (co-crystal) Deposited 2025-09-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–854（854 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 A1CTW N-{[(2Z,3aS,4S,6Z,7R,10aS)-10,10-dihydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl}benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277.15 K；20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0, STX-C13-NBz:NpSxph molar ratio 1.2:1	Resolution 1.95 Å R-free 0.223
9Y92 Nanorana parkeri saxiphilin:STX-C13-OBz (co-crystal) Deposited 2025-09-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–854（854 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 A1CTG [(2Z,3aS,4R,6Z,7R,10aS)-10,10-dihydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl benzoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277.15 K；20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0, STX-C13-OBz:NpSxph molar ratio 1.2:1	Resolution 1.90 Å R-free 0.226

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

View Construct and Data Evidence

UniProt name	A0A9X9ZA84_9NEOB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–854； UniProt 1–854

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	8v68
Deposition date deposition_date	2023-12-01
最后修订 last_revision	2025-05-07
Structure title title	Nanorana parkeri saxiphilin:dcSTX (co-crystal)
Keywords keywords	Saxiphilin, Toxin resistance, Saxitoxin, ANTITOXIN; ANTITOXIN
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	32.57 Å
Radius of gyration Rg (electron density) rg_electron	32.00 Å
Forward intensity I(0) i0	265136000.00
Molecular weight molecular_weight	85378.0 kDa
Excluded volume excluded_volume	81594 Å³
Envelope volume envelope_volume	147370 Å³
Hydration-shell volume shell_volume	38678 Å³
Envelope diameter envelope_diameter	106.7 Å
Shell Rg shell_rg	38.74 Å
Envelope Rg envelope_rg	31.46 Å
Shape Rg shape_rg	31.98 Å
Total Rg total_rg	32.43 Å
Total atoms total_atoms	6416
Residues n_residues	823
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	105.9 Å
Rg (real space) rg_real	32.55 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	2.6510e+08
I(0) uncertainty (real space) i0_real_error	4.4790e+06
Rg (reciprocal space) rg_reciprocal	32.56 Å
I(0) (reciprocal space) i0_reciprocal	265100000.0000
Solution quality estimate total_estimate	0.9008
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.9 Å
Skewness Skewness skewness	0.275
Kurtosis Kurtosis kurtosis	-0.524
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	17600000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.930

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Saxiphilin
Molecular weight formula_weight	94703.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6826

MALTFHTALYFTIVGLSFAASDARHVQWCTISHLEQKKCNDLVGSCNVPDITLACVYRSSTENCMAAIKDGQADAMFLDSGDVYKASLDHYNLKPIIAEPYSLHRELTKCLKHRQESLGGDKMVKGRYIPQCDEKGNYHPVQCHASTGYCWCVNANGEKIEGTNTTPVQTPPTCPSQVLTKCLKERQEALGGKRIAIGRYIPQCDEQGNYRPMQCHGSTGYCWCVNAIGEKIEGTNTPPGNTQPTCQSHDWDTCHYAVAVVKNSSTFQFGQLKGKRSCHSGLSKTDGWNAPVNVFVEKKLLPWDGLAKGSIERAVSKFFSASCIPGATETNLCKQCIGEEEKKCKSSHDEPYYGDHGAFRCLQEDKGDVAFLKNTALPDEHSGVYELLCPDNTRKPLNKYKECNLGKVPADAVVTRKAGDKTKDINDFLLEAQKKKCKLFGSPHGKDLMFDDSTTHLAPLPSEIDAFFFLGVKWYNAMKALTEDVKLPSKNKVRWCTINKPEMMKCKDWAAVSGGAIACTEASCPEHCVKQILKGEADAVTLDVQYMYMALMCGLLPAVEEYPNKDDFHPCQIPGSTIKDFGTKRAVALVKKSNKDIKWNNLKGKKSCHTHVGDIPGWVIPAGLISNQNDNIDIESFFGESCAPGSDTNSKLCKLCIGDPENPKASTRCSLSDKEAYYGNEGAFRCLVEKGDVAFVPHTVVFANTDGKNPAEWAKDLKSEDFEILCLDGSRAPVTNYRGCNLSGLPPRAIVTREESVSDVVRILINQQSLYGRNGFEKDMFQMFSSAKGQNLLFNDETQCLIEFDRQPKDIMEDYFGVRYYTAVYSASRSAVPSELIPACTFKHCSNSLEVLFQ

来源 Source

来源生物 organism	Nanorana parkeri
NCBI Class编号 ncbi_taxonomy_id	125878
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	(3aS,4R,7R,10aS)-2,6-diamino-4-(hydroxymethyl)-3a,4,8,9-tetrahydro-1H,10H-pyrrolo[1,2-c]purine-10,10-diol
Molecular weight formula_weight	256.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	400

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8. Citations (1)

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Unit-cell length a length_a	229.473 Å
Unit-cell length b length_b	229.473 Å
Unit-cell length c length_c	67.605 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	43.370 Å
R factor r_factor	0.1973
R_work r_work	0.1968
R_free r_free	0.2246

fit	/app/data/saxs_computation/v6/8v68/8v68.fit
pddf	/app/data/pr_computation/v6/8v68/8v68.pr.out
profile	/app/data/saxs_computation/v6/8v68/8v68.dat

Nanorana parkeri saxiphilin:dcSTX (co-crystal)

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

Saxiphilin

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