9ZRB | pdb_00009zrb

Crystal structure of macrodomain from Chikungunya virus in complex with Adenosine diphosphate ribose

PDB DOI: https://doi.org/10.2210/pdb9ZRB/pdb

Classification: VIRAL PROTEIN
Organism(s): Chikungunya 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.192 (Depositor), 0.194 (DCC)
R-Value Work:
0.152 (Depositor), 0.153 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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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 macrodomain from Chikungunya virus

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

To be published.

Macromolecule Content

Total Structure Weight: 75.23 kDa
Atom Count: 5,862
Modeled Residue Count: 640
Deposited Residue Count: 640
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein P1234	A, B, C, D	160	Chikungunya virus	Mutation(s): 0
UniProt
Find proteins for A0A7S9AU77 (Chikungunya virus) Explore A0A7S9AU77 Go to UniProtKB: A0A7S9AU77
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7S9AU77
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 Query on AR6 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain M [auth B]	G [auth A], M [auth B], Q [auth C], S [auth D]	[(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		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D]
APR (Subject of Investigation/LOI) Query on APR Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D]	F [auth A], L [auth B], P [auth C], R [auth D]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain R [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	J [auth B], O [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain J [auth B] Focus chain O [auth C]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain T [auth D]	E [auth A] H [auth B] I [auth B] K [auth B] N [auth C] E [auth A], H [auth B], I [auth B], K [auth B], N [auth C], T [auth D]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D]