9IQ4 | pdb_00009iq4

Crystal structure of African swine fever virus methyltransferase EP424R in complex with S-Adenosylhomocysteine

PDB DOI: https://doi.org/10.2210/pdb9IQ4/pdb

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

Deposited: 2024-07-12 Released: 2025-08-13
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: 2.42 Å
R-Value Free:
0.212 (Depositor), 0.216 (DCC)
R-Value Work:
0.205 (Depositor), 0.208 (DCC)
R-Value Observed:
0.205 (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 S-Adenosylhomocysteine

Wang, Z.X., Guo, F.L., Liu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 98.03 kDa
Atom Count: 6,739
Modeled Residue Count: 786
Deposited Residue Count: 836
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase EP424R	A, B	418	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
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.212 (Depositor), 0.216 (DCC)
R-Value Work: 0.205 (Depositor), 0.208 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.113	α = 90
b = 56.918	β = 112.3
c = 100.465	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPX	data reduction
PHENIX	phasing
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-13

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: 2025-08-13
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.