9YHC | pdb_00009yhc

Crystal structure of Chikungunya virus nsP3 macrodomain D31H mutant (P31 crystal form)

PDB DOI: https://doi.org/10.2210/pdb9YHC/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: 1.35 Å
R-Value Free:
0.172 (Depositor), 0.173 (DCC)
R-Value Work:
0.136 (Depositor), 0.139 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 75.56 kDa
Atom Count: 5,921
Modeled Residue Count: 657
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

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(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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain E [auth A]	E [auth A], L [auth B], Q [auth C], V [auth D], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain X [auth D] SDF format, chain R [auth C] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain X [auth D] MOL2 format, chain R [auth C] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain X [auth D] mmCIF format, chain R [auth C]	F [auth A], M [auth B], R [auth C], X [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain K [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain K [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain K [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C], Y [auth D], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D]