9YHD | pdb_00009yhd

Crystal structure of Chikungunya virus nsP3 macrodomain D31N mutant (P41 crystal form) in complex with ADP-ribose

PDB DOI: https://doi.org/10.2210/pdb9YHD/pdb

Classification: VIRAL PROTEIN,HYDROLASE
Organism(s): Chikungunya virus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-09-30 Released: 2025-11-26
Deposition Author(s): Correy, G.J., Fraser, J.S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.249 (Depositor), 0.249 (DCC)
R-Value Work:
0.186 (Depositor), 0.186 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

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 Chikungunya virus nsP3 macrodomain D31H mutant (P31 crystal form)

Correy, G.J., Fraser, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 75.1 kDa
Atom Count: 5,384
Modeled Residue Count: 640
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B, C, D	168	Chikungunya virus	Mutation(s): 1 EC: 3.1.3.84
UniProt
Find proteins for Q8JUX6 (Chikungunya virus (strain S27-African prototype)) Explore Q8JUX6 Go to UniProtKB: Q8JUX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8JUX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APR (Subject of Investigation/LOI) Query on APR Download Ideal Coordinates CCD File SDF format, chain E [auth D] MOL2 format, chain E [auth D] mmCIF format, chain E [auth D]	E [auth D]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain E [auth D] Interactions & Density Focus chain E [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.249 (Depositor), 0.249 (DCC)
R-Value Work: 0.186 (Depositor), 0.186 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.474	α = 90
b = 73.474	β = 90
c = 114.228	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	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 Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171110

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.