9BZ1 | pdb_00009bz1

Cocrystal structure of Clostridium beijerinckii ZTP riboswitch with AICA

PDB DOI: https://doi.org/10.2210/pdb9BZ1/pdb
NAKB: 9BZ1

Classification: RNA
Organism(s): Clostridium beijerinckii
Expression System: in vitro transcription vector pT7-Fluc(deltai)
Mutation(s): No

Deposited: 2024-05-24 Released: 2024-11-27
Deposition Author(s): Jones, C.J., Ferre D'Amare, A.R., Tran, B.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.248 (Depositor), 0.249 (DCC)
R-Value Work:
0.209 (Depositor), 0.211 (DCC)
R-Value Observed:
0.212 (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

Cocrystal structure of Clostridium beijerinckii ZTP riboswitch with AICA

Jones, C.P., Tran, B., Ferre-D'Amare, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 58.01 kDa
Atom Count: 3,643
Modeled Residue Count: 168
Deposited Residue Count: 178
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (84-MER)	A, B	89	Clostridium beijerinckii
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5AC (Subject of Investigation/LOI) Query on 5AC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	G [auth A], M [auth B]	5-amino-1H-imidazole-4-carboxamide C₄ H₆ N₄ O DVNYTAVYBRSTGK-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]
K Query on K Download:Ideal Coordinates CCD File 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 Q [auth B] SDF format, chain R [auth B] SDF format, chain P [auth B] 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 Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] 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 Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B]	H [auth A] I [auth A] J [auth A] N [auth B] O [auth B] H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] K [auth B] C [auth A], D [auth A], E [auth A], F [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]