9ybd

Rana catesbeiana saxiphilin mutant - F561A:STX-C13-OBz (co-crystal)

Method: X-RAY DIFFRACTION D_max: 147.9 Å Quality: GOOD

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

Saxiphilin

Aquarana catesbeiana

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 1–844	Mutation：F561A	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 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX-C13-OBz:Saxiphilin molar ratio 1.1:1	Resolution 2.40 Å R-free 0.258
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–844	Mutation：F561A	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 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX-C13-OBz:Saxiphilin molar ratio 1.1:1	Resolution 2.40 Å R-free 0.258

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 9YBD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6O0D Saxiphilin Apo structure Deposited 2019-02-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 40% 2-methyl-2,4-pentanediol (MPD)	Resolution 2.50 Å R-free 0.253
6O0D Saxiphilin Apo structure Deposited 2019-02-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 40% 2-methyl-2,4-pentanediol (MPD)	Resolution 2.50 Å R-free 0.253
6O0E Saxiphilin:STX complex, soaking Deposited 2019-02-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Not recorded	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 40% 2-methyl-2,4-pentanediol (MPD). 1mM final concentration of STX was added during soaking	Resolution 2.50 Å R-free 0.262
6O0E Saxiphilin:STX complex, soaking Deposited 2019-02-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Not recorded	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 40% 2-methyl-2,4-pentanediol (MPD). 1mM final concentration of STX was added during soaking	Resolution 2.50 Å R-free 0.262
6O0F Saxiphilin:STX complex, co-crystal Deposited 2019-02-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Not recorded	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 40% 2-methyl-2,4-pentanediol (MPD). STX: Saxiphilin molar ratio 1:1.1	Resolution 2.12 Å R-free 0.259
6O0F Saxiphilin:STX complex, co-crystal Deposited 2019-02-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Not recorded	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 40% 2-methyl-2,4-pentanediol (MPD). STX: Saxiphilin molar ratio 1:1.1	Resolution 2.12 Å R-free 0.259
8D6P Rana catesbeiana saxiphilin mutant - Y558A Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Mutation：Y558A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD	Resolution 2.60 Å R-free 0.264
8D6P Rana catesbeiana saxiphilin mutant - Y558A Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Mutation：Y558A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD	Resolution 2.60 Å R-free 0.264
8D6Q Rana catesbeiana saxiphilin mutant - Y558I Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Mutation：Y558I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 27% MPD	Resolution 2.70 Å R-free 0.272
8D6Q Rana catesbeiana saxiphilin mutant - Y558I Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Mutation：Y558I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 27% MPD	Resolution 2.70 Å R-free 0.272
8D6S Rana catesbeiana saxiphilin mutant - Y558A:STX (co-crystal) Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Mutation：Y558A	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX:Saxiphilin molar ratio 1.1:1	Resolution 2.60 Å R-free 0.262
8D6S Rana catesbeiana saxiphilin mutant - Y558A:STX (co-crystal) Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Mutation：Y558A	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX:Saxiphilin molar ratio 1.1:1	Resolution 2.60 Å R-free 0.262
8D6T Rana catesbeiana saxiphilin mutant - Y558I:STX (co-crystal) Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Mutation：Y558I	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1 CAC CACODYLATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 27% MPD, STX:Saxiphilin molar ratio 1.1:1	Resolution 2.15 Å R-free 0.234
8D6T Rana catesbeiana saxiphilin mutant - Y558I:STX (co-crystal) Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Mutation：Y558I	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1 CAC CACODYLATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 27% MPD, STX:Saxiphilin molar ratio 1.1:1	Resolution 2.15 Å R-free 0.234
8D6U Rana catesbeiana saxiphilin:F-STX (soaked) Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Not recorded	QDX (2P)-4-({6-[({[(3aS,4R,7R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methoxy}carbonyl)amino]hexyl}carbamoyl)-2-{[4aP,9(9a)P]-6-hydroxy-3-oxo-3H-xanthen-9-yl}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.11-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, 1 mM (final concentration) F-STX was added during soaking	Resolution 2.65 Å R-free 0.266
8D6U Rana catesbeiana saxiphilin:F-STX (soaked) Deposited 2022-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Not recorded	QDX (2P)-4-({6-[({[(3aS,4R,7R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methoxy}carbonyl)amino]hexyl}carbamoyl)-2-{[4aP,9(9a)P]-6-hydroxy-3-oxo-3H-xanthen-9-yl}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.11-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, 1 mM (final concentration) F-STX was added during soaking	Resolution 2.65 Å R-free 0.266
9YAR Rana catesbeiana saxiphilin:STX-C13-OBz (co-crystal) Deposited 2025-09-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Not recorded	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 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 27% MPD, STX-C13-OBz:Saxiphilin molar ratio 1.1:1	Resolution 2.40 Å R-free 0.278
9YAR Rana catesbeiana saxiphilin:STX-C13-OBz (co-crystal) Deposited 2025-09-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Not recorded	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 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 27% MPD, STX-C13-OBz:Saxiphilin molar ratio 1.1:1	Resolution 2.40 Å R-free 0.278
9YAS Rana catesbeiana saxiphilin mutant - Y558A:STX-C13-OBz (co-crystal) Deposited 2025-09-16	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Mutation：Y558A	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 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX-C13-OBz:Saxiphilin molar ratio 1.1:1	Resolution 2.45 Å R-free 0.284
9YAS Rana catesbeiana saxiphilin mutant - Y558A:STX-C13-OBz (co-crystal) Deposited 2025-09-16	Different mutation/modification Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Mutation：Y558A	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 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX-C13-OBz:Saxiphilin molar ratio 1.1:1	Resolution 2.45 Å R-free 0.284
9YAT Rana catesbeiana saxiphilin mutant - T563A Deposited 2025-09-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Mutation：T563A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD	Resolution 2.50 Å R-free 0.246
9YAT Rana catesbeiana saxiphilin mutant - T563A Deposited 2025-09-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Mutation：T563A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD	Resolution 2.50 Å R-free 0.246
9YAV Rana catesbeiana saxiphilin mutant - F561A Deposited 2025-09-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Mutation：F561A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD	Resolution 2.23 Å R-free 0.244
9YAV Rana catesbeiana saxiphilin mutant - F561A Deposited 2025-09-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Mutation：F561A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD	Resolution 2.23 Å R-free 0.244
9YBE Rana catesbeiana saxiphilin mutant - F561A:STX (co-crystal) Deposited 2025-09-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Mutation：F561A	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX:Saxiphilin molar ratio 1.1:1	Resolution 2.35 Å R-free 0.274
9YBE Rana catesbeiana saxiphilin mutant - F561A:STX (co-crystal) Deposited 2025-09-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Mutation：F561A	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX:Saxiphilin molar ratio 1.1:1	Resolution 2.35 Å R-free 0.274
9YBF Rana catesbeiana saxiphilin mutant - T563A:STX-C13-OBz (co-crystal) Deposited 2025-09-17	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–844（844 aa）	Mutation：T563A	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 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX-C13-OBz:Saxiphilin molar ratio 1.1:1	Resolution 2.45 Å R-free 0.263
9YBF Rana catesbeiana saxiphilin mutant - T563A:STX-C13-OBz (co-crystal) Deposited 2025-09-17	Different mutation/modification Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–844（844 aa）	Mutation：T563A	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 6.5；277.15 K；0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX-C13-OBz:Saxiphilin molar ratio 1.1:1	Resolution 2.45 Å R-free 0.263

14 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SAX_LITCT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–844； UniProt 1–844 Author chain B； PDBConstruct 1–844； UniProt 1–844

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ybd
Deposition date deposition_date	2025-09-17
最后修订 last_revision	2026-05-27
Structure title title	Rana catesbeiana saxiphilin mutant - F561A:STX-C13-OBz (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	44.76 Å
Radius of gyration Rg (electron density) rg_electron	44.44 Å
Forward intensity I(0) i0	1010430000.00
Molecular weight molecular_weight	170400.0 kDa
Excluded volume excluded_volume	162630 Å³
Envelope volume envelope_volume	334690 Å³
Hydration-shell volume shell_volume	62218 Å³
Envelope diameter envelope_diameter	150.7 Å
Shell Rg shell_rg	49.91 Å
Envelope Rg envelope_rg	43.34 Å
Shape Rg shape_rg	44.43 Å
Total Rg total_rg	44.62 Å
Total atoms total_atoms	12800
Residues n_residues	1654
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	147.9 Å
Rg (real space) rg_real	44.75 Å
Rg uncertainty (real space) rg_real_error	1.35 Å
I(0) (real space) i0_real	1.0100e+09
I(0) uncertainty (real space) i0_real_error	1.8140e+07
Rg (reciprocal space) rg_reciprocal	44.76 Å
I(0) (reciprocal space) i0_reciprocal	1010000000.0000
Solution quality estimate total_estimate	0.8927
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.7 Å
Skewness Skewness skewness	0.264
Kurtosis Kurtosis kurtosis	-0.537
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	28500000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.833

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Saxiphilin
Molecular weight formula_weight	94152.2 kDa
Mutation mutation	F561A
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	12862

MAPTFQTALFFTIISLSFAAPNAKQVRWCAISDLEQKKCNDLVGSCNVPDITLVCVLRSSTEDCMTAIKDGQADAMFLDSGEVYEASKDPYNLKPIIAEPYSSNRDLQKCLKERQQALAKKMIGHYIPQCDEKGNYQPQQCHGSTGHCWCVNAMGEKISGTNTPPGQTRATCERHELPKCLKERQVALGGDEKVLGRFVPQCDEKGNYEPQQFHGSTGYSWCVNAIGEEIAGTKTPPGKIPATCQKHDLVTTCHYAVAMVKKSSAFQFNQLKGKRSCHSGVSKTDGWKALVTVLVEKKLLSWDGPAKESIQRAMSKFFSVSCIPGATQTNLCKQCKGEEGKNCKNSHDEPYYGNYGAFRCLKEDMGDVAFLRSTALSDEHSEVYELLCPDNTRKPLNKYKECNLGTVPAGTVVTRKISDKTEDINNFLMEAQKRQCKLFSSAHGKDLMFDDSTLQLALLSSEVDAFLYLGVKLFHAMKALTGDAHLPSKNKVRWCTINKLEKMKCDDWSAVSGGAIACTEASCPKGCVKQILKGEADAVKLEVQYMYEALMCGLLPAVEEYHNKDDFGPCKTPGSPYTDAGTLRAVALVKKSNKDINWNNIKGKKSCHTGVGDIAGWVIPVSLIRRQNDNSDIDSFFGESCAPGSDTKSNLCKLCIGDPKNSAANTKCSLSDKEAYYGNQGAFRCLVEKGDVAFVPHTVVFENTDGKNPAVWAKNLKSEDFELLCLDGSRAPVSNYKSCKLSGIPPPAIVTREESISDVVRIVANQQSLYGRKGFEKDMFQLFSSNKGNNLLFNDNTQCLITFDRQPKDIMEDYFGKPYYTTVYGASRSAMSSELISACTIKHCSNSLEVLFQ

来源 Source

来源生物 organism	Aquarana catesbeiana
通用名 common_name	American bullfrog
NCBI Class编号 ncbi_taxonomy_id	8400
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	[(2Z,3aS,4R,6Z,7R,10aS)-10,10-dihydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl benzoate
Molecular weight formula_weight	360.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

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8. Citations (1)

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Unit-cell length a length_a	96.424 Å
Unit-cell length b length_b	110.042 Å
Unit-cell length c length_c	256.010 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	8

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	48.210 Å
R factor r_factor	0.2305
R_work r_work	0.2290
R_free r_free	0.2582

fit	/app/data/saxs_computation/yb/9ybd/9ybd.fit
pddf	/app/data/pr_computation/yb/9ybd/9ybd.pr.out
profile	/app/data/saxs_computation/yb/9ybd/9ybd.dat