9EBP | pdb_00009ebp

Structure of the Bacillus subtilis yjdF riboswitch complexed with lumichrome in the presence of iridium hexammine

PDB DOI: https://doi.org/10.2210/pdb9EBP/pdb

Classification: RNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2024-11-12 Released: 2025-11-19
Deposition Author(s): Batey, R.T., Spradlin, S.F.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.290 (Depositor), 0.292 (DCC)
R-Value Work:
0.247 (Depositor), 0.249 (DCC)
R-Value Observed:
0.252 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of the Bacillus subtilis yjdF riboswitch complexed with lumichrome in the presence of iridium hexammine

Batey, R.T., Spradlin, S.F.

To be published.

Macromolecule Content

Total Structure Weight: 55.85 kDa
Atom Count: 3,603
Modeled Residue Count: 162
Deposited Residue Count: 162
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (81-MER)	A, B [auth M]	81	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IRI Query on IRI Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth M] SDF format, chain L [auth M] SDF format, chain M SDF format, chain N [auth M] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth M] MOL2 format, chain L [auth M] MOL2 format, chain M MOL2 format, chain N [auth M] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth M] mmCIF format, chain L [auth M] mmCIF format, chain M mmCIF format, chain N [auth M]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth M], L [auth M], M, N [auth M]	IRIDIUM HEXAMMINE ION H₁₈ Ir N₆ CGMAOQLDNKCXGK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth M] Focus chain L [auth M] Focus chain M Focus chain N [auth M] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth M] Focus chain L [auth M] Focus chain M Focus chain N [auth M]
LUM (Subject of Investigation/LOI) Query on LUM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth M] MOL2 format, chain C [auth A] MOL2 format, chain J [auth M] mmCIF format, chain C [auth A] mmCIF format, chain J [auth M]	C [auth A], J [auth M]	LUMICHROME C₁₂ H₁₀ N₄ O₂ ZJTJUVIJVLLGSP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth M] Interactions & Density Focus chain C [auth A] Focus chain J [auth M]