8U5T

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

PDB DOI: https://doi.org/10.2210/pdb8U5T/pdb
NAKB: 8U5T

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: 2.20 Å
R-Value Free: 0.233
R-Value Work: 0.188
R-Value Observed: 0.190

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 variant aptamer bound to T01-6A-B

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

To be published.

Macromolecule Content

Total Structure Weight: 38.57 kDa
Atom Count: 2,561
Modelled Residue Count: 108
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 variant	A, B, C	36	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VLR (Subject of Investigation/LOI) Query on VLR Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C]	H [auth A], L [auth B], O [auth C]	3-{2,16-dioxo-20-[(3aS,4R,6aS)-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-FPNRCKICSA-O		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C]
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 I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [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 I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]