2TOB | pdb_00002tob

SOLUTION STRUCTURE OF THE TOBRAMYCIN-RNA APTAMER COMPLEX, NMR, 13 STRUCTURES

• PDB DOI: https://doi.org/10.2210/pdb2TOB/pdb
• NAKB: 2TOB

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


• Deposited: 1998-06-17 Released: 1999-06-22 
• Deposition Author(s): Jiang, L., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 13 
• Selection Criteria: LOWEST NOE AND TOTAL ENERGY 

Literature

Solution structure of the tobramycin-RNA aptamer complex.

Jiang, L., Patel, D.J.

(1998) Nat Struct Biol 5: 769-774

• PubMed: 9731769 
• DOI: https://doi.org/10.1038/1804
• Primary Citation Related Structures: 
  2TOB


• PubMed Abstract: 
  

  We have solved the solution structure of the aminoglycoside antibiotic tobramycin complexed with a stem-loop RNA aptamer. The 14 base loop of the RNA aptamer 'zippers up' alongside the attached stem through alignment of four mismatches and one Watson-Crick pair on complex formation. The tobramycin inserts into the deep groove centered about the mismatch pairs and is partially encapsulated between its floor and a looped out guanine base that flaps over the bound antibiotic. Several potential intermolecular hydrogen bonds between the charged NH3 groups of tobramycin and acceptor atoms on base pair edges and backbone phosphates anchor the aminoglycoside antibiotic within its sequence/structure specific RNA binding pocket.

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Organizational Affiliation: 
• Cellular Biochemistry & Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.94 kDa 
• Atom Count: 457 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*CP*UP*UP*GP*GP*UP*UP*UP*AP*GP*GP*UP*AP*AP*UP*GP*AP*GP*U)-3')	A	20	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TOA	B [auth A]	3-ammonio-3-deoxy-alpha-D-glucopyranose C6 H14 N O5 BQCCAEOLPYCBAE-RXRWUWDJSA-O
2TB	D [auth A]	1,3-DIAMINO-4,5,6-TRIHYDROXY-CYCLOHEXANE C6 H16 N2 O3 DTFAJAKTSMLKAT-JDCCYXBGSA-P
TOC	C [auth A]	2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose C6 H16 N2 O3 CEGXIUROHCNLCL-MOJAZDJTSA-P

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 13 
• Selection Criteria: LOWEST NOE AND TOTAL ENERGY 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-22 
Deposition Author(s): Jiang, L., Patel, D.J.

Revision History  

• Version 1.0: 1999-06-22
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-06-24
  Changes: Database references, Derived calculations, Other, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Structure summary