7REX | pdb_00007rex

PreQ1-1 (type-1) riboswitch in complex with tandem stacked metabolites

PDB DOI: https://doi.org/10.2210/pdb7REX/pdb
NAKB: 7REX

Classification: RNA
Organism(s): Carnobacterium antarcticum
Mutation(s): No

Deposited: 2021-07-13 Released: 2021-12-29
Deposition Author(s): Jenkins, J.L., Schroeder, G.M., Wedekind, J.E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.272 (Depositor), 0.270 (DCC)
R-Value Work:
0.232 (Depositor), 0.230 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

Schroeder, G.M., Cavender, C.E., Blau, M.E., Jenkins, J.L., Mathews, D.H., Wedekind, J.E.

(2022) Nat Commun 13: 199

DOI: https://doi.org/10.1038/s41467-021-27790-8

Macromolecule Content

Total Structure Weight: 33.72 kDa
Atom Count: 2,125
Modeled Residue Count: 97
Deposited Residue Count: 102
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (34-MER)	A, B, C	34	Carnobacterium antarcticum
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRF (Subject of Investigation/LOI) Query on PRF Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain D [auth A]	D [auth A] E [auth A] I [auth B] J [auth B] K [auth C] D [auth A], E [auth A], I [auth B], J [auth B], K [auth C], L [auth C]	7-DEAZA-7-AMINOMETHYL-GUANINE C₇ H₉ N₅ O MEYMBLGOKYDGLZ-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 C] Focus chain L [auth C] 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 C] Focus chain L [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth C]	F [auth A], G [auth A], H [auth A], M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C]