NMR Ensemble

1QD3

HIV-1 TAR RNA/NEOMYCIN B COMPLEX

Structural Biology Knowledgebase: 1QD3 SBKB.org


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100
  • Conformers Submitted: 17
  • Selection Criteria: Lowest Energy Agreement with Experimental Data

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1QD3

Classification: RNA

Total Structure Weight: 9959.28

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 TAR RNA A 29 Human immunodeficiency virus 1 NEOMYCIN B (RESIDUES BDG-CYY-RYB-IDG) COMPLEXED IN THE RNA MINOR GROOVE

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

A 2-DEOXYSTREPTAMINE
C6 H14 N2 O3
DTFAJAKTSMLKAT-JDCCYXBGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RIB
Query on RIB

A RIBOSE
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RIB N/A in BindingDB
N/A in BindingMoad
Kd: 5900 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100
  • Conformers Submitted: 17
  • Selection Criteria: LOWEST ENERGY, AGREEMENT WITH EXPERIMENTAL DATA

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1999-07-07
  • Released Date: 2000-07-12
  • Deposition author(s): Faber, C., Sticht, H., Roesch, P.

Revision History

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