7EI8 | pdb_00007ei8

RNA kink-turn motif with 2-aminopurine

PDB DOI: https://doi.org/10.2210/pdb7EI8/pdb
NAKB: 7EI8

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

Deposited: 2021-03-30 Released: 2022-03-30
Deposition Author(s): Kondo, J., Saisu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure-based design of a sequence-specific RNA probe that mimics the kink-turn motif

Miyauchi, T., Yamaguchi, K., Saisu, S., Kondo, J.

(2025) Nar Mol Med 2

DOI: https://doi.org/10.1093/narmme/ugaf006

Macromolecule Content

Total Structure Weight: 25.38 kDa
Atom Count: 1,646
Modeled Residue Count: 76
Deposited Residue Count: 76
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(GPGPC)-D(P(2PR)P(2PR)P(2PR)P(2PR))-R(PAPAPCPCPGPGPGPGPAPGPCP*C)-3')	A, B, C, D	19	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain L [auth C] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain L [auth C] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain L [auth C] mmCIF format, chain G [auth B]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth B] E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth C], K [auth C], L [auth C], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth D], R [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D]