NMR Ensemble

1NEM

Saccharide-RNA recognition in the neomycin B / RNA aptamer complex

Structural Biology Knowledgebase: 1NEM SBKB.org


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100
  • Conformers Submitted: 9
  • Selection Criteria: Least Restraint Violation

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NEM

Classification: RNA

Total Structure Weight: 8111.22

Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP*AP*GP*UP*CP*C)-3' A 23 synthetic Complexed with neomycin B; hetero groups BDG (ring A), NEB (ring B), RIB (ring C), and NED (ring D)

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
IDG
Query on IDG

A O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE
C6 H14 N2 O4
SQTHUUHOUPJYLK-BSQWINAVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BDG
Query on BDG

A O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE
C6 H14 N2 O4
SQTHUUHOUPJYLK-UKFBFLRUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NEB
Query on NEB

A 2-DEOXY-D-STREPTAMINE
C6 H15 N2 O3
DTFAJAKTSMLKAT-JDCCYXBGSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BDR
Query on BDR

A BETA-D-RIBOFURANOSYL
C5 H10 O5
HMFHBZSHGGEWLO-TXICZTDVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100
  • Conformers Submitted: 9
  • Selection Criteria: LEAST RESTRAINT VIOLATION

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1999-03-15
  • Released Date: 1999-08-31
  • Deposition author(s): Jiang, L., Majumdar, A., Hu, W., Jaishree, T.J., Xu, W., Patel, D.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4