1TOB

SACCHARIDE-RNA RECOGNITION IN AN AMINOGLYCOSIDE ANTIBIOTIC-RNA APTAMER COMPLEX, NMR, 7 STRUCTURES

• PDB DOI: https://doi.org/10.2210/pdb1TOB/pdb
• NAKB: 1TOB

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


• Deposited: 1996-12-12 Released: 1997-06-16 
• Deposition Author(s): Jiang, L., Suri, A.K., Fiala, R., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 7 
• Selection Criteria: ENERGY (INCLUDING RESTRAINT ENERGY TERM) 

Literature

Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex.

Jiang, L., Suri, A.K., Fiala, R., Patel, D.J.

(1997) Chem Biol 4: 35

• PubMed: 9070426 
• DOI: https://doi.org/10.1016/s1074-5521(97)90235-0
• Primary Citation of Related Structures:  
  1TOB


• PubMed Abstract: 
  

  Aminoglycoside antibiotics are known to target ribosomal, retroviral and catalytic RNAs with high affinity and specificity. Recently, in vitro selection experiments have identified RNA aptamers that bind to aminoglycoside antibiotics with nanomolar affinity and stringent specificity, allowing discrimination between closely related family members. There has, to date, been limited structural information on the molecular basis of such saccharide-RNA recognition.

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Organizational Affiliation: 

Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, new York, NY 10021, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.13 kDa 
• Atom Count: 603 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(GGCACGAGGUUUAGCUACACUCGUGCC)-3')	A	27	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
TOC	C [auth A]	2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose C6 H16 N2 O3 CEGXIUROHCNLCL-MOJAZDJTSA-P
TOB	D [auth A]	1,3-DIAMINO-5,6-DIHYDROXYCYCLOHEXANE C6 H16 N2 O2 QOLDZWBHLDQIJR-FSIIMWSLSA-P

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 7 
• Selection Criteria: ENERGY (INCLUDING RESTRAINT ENERGY TERM) 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-06-16 
Deposition Author(s): Jiang, L., Suri, A.K., Fiala, R., Patel, D.J.

Revision History  

• Version 1.0: 1997-06-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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