Macromolecule Content

Total Structure Weight: 74.75 kDa
Atom Count: 5054
Residue Count: 638
Unique protein chains: 1

6W8K

Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments

DOI: 10.2210/pdb6W8K/pdb

Classification: VIRAL PROTEIN
Organism(s): Chikungunya virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-20 Released: 2021-01-13
Deposition Author(s): Zhang, S., Garzan, A., Augelli-Szafran, C.E., Pathak, A.K., Wu, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.248
R-Value Work: 0.210
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Literature

Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design

Zhang, S., Garzan, A., Augelli-Szafran, C.E., Pathak, A.K., Wu, M.

(2020) PLoS One

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nonstructural polyprotein	A, B, C, D	168	Chikungunya virus	Mutation(s): 0 EC: 2.7.7.19 (UniProt), 3.1.3.33 (UniProt), 3.1.3.84 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
Find proteins for A0A4D6GPC4 (Chikungunya virus) Explore A0A4D6GPC4 Go to UniProtKB: A0A4D6GPC4
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TJ4 Query on TJ4 Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain F [B] SDF format, chain G [C] SDF format, chain H [D] MOL2 format, chain E [A] MOL2 format, chain F [B] MOL2 format, chain G [C] MOL2 format, chain H [D]	A, B, C, D	5,6-dimethyl-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid C₇ H₈ N₂ O₃ ZXECTTZQEACQGR-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.248
R-Value Work: 0.210
R-Value Observed: 0.211
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.013	α = 90
b = 88.013	β = 90
c = 83.552	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-03-20
Released Date: 2021-01-13

Deposition Author(s):

Augelli-Szafran, C.E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1U19AI142759-01

Revision History

Version 1.0: 2021-01-13
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.