8K85 | pdb_00008k85

Crystal structure of Red Broccoli aptamer with OBI

PDB DOI: https://doi.org/10.2210/pdb8K85/pdb
NAKB: 8K85

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

Deposited: 2023-07-28 Released: 2025-02-12
Deposition Author(s): Peng, X., Huang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.249 (Depositor), 0.260 (DCC)
R-Value Work:
0.197 (Depositor), 0.210 (DCC)
R-Value Observed:
0.199 (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

Structural analysis of various Broccoli aptamers with different Fluorophores

Peng, X., Huang, L.

To be published.

Macromolecule Content

Total Structure Weight: 37.5 kDa
Atom Count: 2,484
Modeled Residue Count: 112
Deposited Residue Count: 112
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (56-MER)	A, B	56	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EBI Query on A1EBI Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	(5Z)-3-(3H-benzimidazol-4-ylmethyl)-5-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]methylidene]-2-[(E)-hydroxyiminomethyl]imidazol-4-one C₁₉ H₁₃ F₂ N₅ O₃ MWUNZPXNBRYTBM-LSGIWYNDSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]