22MT | pdb_000022mt

Crystal structure of the c-di-GMP-II Riboswitch c-di-GMP-II-Bh bound with 2',3'-cGAMP

PDB DOI: https://doi.org/10.2210/pdb22MT/pdb

Classification: RNA
Organism(s): Halalkalibacterium halodurans C-125
Expression System: in vitro transcription vector pT7-TP(deltai)
Mutation(s): No

Deposited: 2026-01-16 Released: 2026-10-21
Deposition Author(s): Cheng, W., Xu, X.C., Patel, D.J., Ren, A.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.231 (Depositor), 0.233 (DCC)
R-Value Work:
0.199 (Depositor), 0.204 (DCC)
R-Value Observed:
0.201 (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 the c-di-GMP-II Riboswitch BhP1-5delC bound with 2',3'-cGAMP

Cheng, W., Xu, X.C., Patel, D.J., Ren, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 51.35 kDa
Atom Count: 3,398
Modeled Residue Count: 150
Deposited Residue Count: 154
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (77-MER)	A, B	77	Halalkalibacterium halodurans C-125
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1SY (Subject of Investigation/LOI) Query on 1SY Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	cGAMP C₂₀ H₂₄ N₁₀ O₁₃ P₂ XRILCFTWUCUKJR-INFSMZHSSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]