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9y92

Nanorana parkeri saxiphilin:STX-C13-OBz (co-crystal)

Method: X-RAY DIFFRACTION Dmax: 105.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Saxiphilin

Nanorana parkeri

UniProt A0A9X9ZA84

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 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

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 9Y92 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
8V68 Nanorana parkeri saxiphilin:dcSTX (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 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
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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9y92

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9y92
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9y92
Deposition date deposition_date2025-09-12
最后修订 last_revision2026-05-27
Structure title titleNanorana parkeri saxiphilin:STX-C13-OBz (co-crystal)
Keywords keywordsSaxiphilin, Toxin resistance, Saxitoxin, ANTITOXIN; ANTITOXIN
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_guinier32.43 Å
Radius of gyration Rg (electron density) rg_electron31.86 Å
Forward intensity I(0) i0263059000.00
Molecular weight molecular_weight85246.0 kDa
Excluded volume excluded_volume81617 ų
Envelope volume envelope_volume145630 ų
Hydration-shell volume shell_volume38411 ų
Envelope diameter envelope_diameter107.2 Å
Shell Rg shell_rg38.58 Å
Envelope Rg envelope_rg31.31 Å
Shape Rg shape_rg31.82 Å
Total Rg total_rg32.32 Å
Total atoms total_atoms6427
Residues n_residues821
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 dmax105.4 Å
Rg (real space) rg_real32.41 Å
Rg uncertainty (real space) rg_real_error0.69 Å
I(0) (real space) i0_real2.6310e+08
I(0) uncertainty (real space) i0_real_error4.0580e+06
Rg (reciprocal space) rg_reciprocal32.42 Å
I(0) (reciprocal space) i0_reciprocal263100000.0000
Solution quality estimate total_estimate0.9005
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.7 Å
Skewness Skewness skewness0.278
Kurtosis Kurtosis kurtosis-0.518
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17310000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.926
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)