9YBE | pdb_00009ybe

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

PDB DOI: https://doi.org/10.2210/pdb9YBE/pdb

Classification: ANTITOXIN
Organism(s): Aquarana catesbeiana
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2025-09-17 Released: 2026-05-27
Deposition Author(s): Chen, Z., Zakrzewska, S., Minor, D.L.
Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.274 (Depositor), 0.274 (DCC)
R-Value Work:
0.240 (Depositor), 0.240 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

Chen, Z., Zakrzewska, S., Minor, D.L.

To be published.

Macromolecule Content

Total Structure Weight: 188.9 kDa
Atom Count: 13,061
Modeled Residue Count: 1,652
Deposited Residue Count: 1,706
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Saxiphilin	A, B	853	Aquarana catesbeiana	Mutation(s): 1
UniProt
Find proteins for P31226 (Aquarana catesbeiana) Explore P31226 Go to UniProtKB: P31226
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31226
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9SL (Subject of Investigation/LOI) Query on 9SL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	[(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 C₁₀ H₁₇ N₇ O₄ RPQXVSUAYFXFJA-HGRQIUPRSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.274 (Depositor), 0.274 (DCC)
R-Value Work: 0.240 (Depositor), 0.240 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.062	α = 90
b = 105.111	β = 90
c = 253.263	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	HDTRA-1-19-1-0040
Department of Defense (DOD, United States)	United States	HDTRA-1-21-1-10011
Department of Defense (DOD, United States)	United States	HDTRA-1-23-1-0026

Revision History (Full details and data files)

Version 1.0: 2026-05-27
Type: Initial release

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