9ZRD | pdb_00009zrd

Crystal structure of macrodomain from Eastern Equine Encephalitis Virus in complex with Adenosine diphosphate ribose

• PDB DOI: https://doi.org/10.2210/pdb9ZRD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Eastern equine encephalitis virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-12-19 Released: 2026-08-12 
• Deposition Author(s): Chang, C., Endre, M., Stols, L., Kim, Y., Joachimiak, A.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of macrodomain from Eastern Equine Encephalitis Virus in complex with Adenosine diphosphate ribose

Chang, C., Endre, M., Stols, L., Kim, Y., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.52 kDa 
• Atom Count: 1,400 
• Modeled Residue Count: 156 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein P1234	A	158	Eastern equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for Q66580 (Eastern equine encephalitis virus) Explore Q66580  Go to UniProtKB:  Q66580

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6	D [auth A]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
APR (Subject of Investigation/LOI)	C [auth A]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.925	α = 90
b = 47.462	β = 90
c = 66.421	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-12 
Deposition Author(s): Chang, C., Endre, M., Stols, L., Kim, Y., Joachimiak, A.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2026-08-12
  Type: Initial release