8U5P

Structure of Mango II aptamer bound to T01-6A-B

PDB DOI: https://doi.org/10.2210/pdb8U5P/pdb
NAKB: 8U5P

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

Deposited: 2023-09-12 Released: 2024-03-27
Deposition Author(s): Passalacqua, L.F.M., Ferre-D'Amare, A.R.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.223
R-Value Work: 0.213
R-Value Observed: 0.216

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

Structure of Mango II aptamer bound to T01-6A-B

Passalacqua, L.F.M., Ferre-D'Amare, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 37.02 kDa
Atom Count: 2,374
Modelled Residue Count: 107
Deposited Residue Count: 108
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Mango II	A, B, C	36	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VKI (Subject of Investigation/LOI) Query on VKI Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	3-[2,16-dioxo-20-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)-6,9,12-trioxa-3,15-diazaicosan-1-yl]-2-{(E)-[6-(4-methoxyphenyl)-1-methylquinolin-4(1H)-ylidene]methyl}-1,3-benzothiazol-3-ium C₄₅ H₅₅ N₆ O₇ S₂ WHIFPTXUSZXQNM-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
K Query on K 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 H [auth B] 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 M [auth C] MOL2 format, chain D [auth A] 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 B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C]