9W7G | pdb_00009w7g

Crystal structure of African swine fever virus methyltransferase EP424R in complex with sinefungin

PDB DOI: https://doi.org/10.2210/pdb9W7G/pdb

Classification: TRANSFERASE
Organism(s): African swine fever virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-06 Released: 2025-11-26
Deposition Author(s): Wang, Z.X., Guo, F.L., Liu, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.229 (Depositor), 0.226 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of African swine fever virus methyltransferase EP424R in complex with sinefungin

Wang, Z.X., Guo, F.L., Liu, Y., Peng, G.Q.

To be published.

Macromolecule Content

Total Structure Weight: 100.62 kDa
Atom Count: 6,673
Modeled Residue Count: 780
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable methyltransferase EP424R	A, B	426	African swine fever virus	Mutation(s): 0 Gene Names: EP424R CDS, EP424R, ASFV-Georgia_4-079
UniProt
Find proteins for A0A2X0RUW3 (African swine fever virus) Explore A0A2X0RUW3 Go to UniProtKB: A0A2X0RUW3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2X0RUW3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFG (Subject of Investigation/LOI) Query on SFG 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]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-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: 2.88 Å
R-Value Free: 0.229 (Depositor), 0.226 (DCC)
R-Value Work: 0.177 (Depositor), 0.178 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.211	α = 90
b = 57.777	β = 112.05
c = 101.912	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-11-26
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.