8U5J

Structure of Mango III variant aptamer bound to T01-07M-B

• PDB DOI: https://doi.org/10.2210/pdb8U5J/pdb
• NAKB: 8U5J

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.236 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 

Literature

Structure of Mango III variant aptamer bound to T01-07M-B

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

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.65 kDa 
• Atom Count: 987 
• Modelled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Mango III variant	A	36	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W6F (Subject of Investigation/LOI)	E [auth A]	2-[(E)-(1,7-dimethylquinolin-4(1H)-ylidene)methyl]-3-{2,16-dioxo-20-[(3aR,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium C39 H51 N6 O6 S2 OPDJCBUXWAHTAM-PJXAABHXSA-O
DMS	C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.236 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.66	α = 90
b = 55.66	β = 90
c = 65.715	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
DIALS	data reduction
DIALS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Passalacqua, L.F.M., Ferre-D'Amare, A.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	--

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release