1DB6

SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE

Structural Biology Knowledgebase: 1DB6 SBKB.org


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30
  • Conformers Submitted: 10
  • Selection Criteria: Structures with Acceptable Covalent Geometry Structures with Favorable Non Bond Energy Structures with the Least Restraint Violations Structures with the Lowest Energy

Literature

Macromolecules
Sequence Display for 1DB6

Classification: DNA

Total Structure Weight: 6903.61

Macromolecule Entities
Molecule Chains Length Organism Details
DNA A 22 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AAR
Query on AAR

A ARGININEAMIDE
C6 H16 N5 O
ULEBESPCVWBNIF-BYPYZUCNSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AAR N/A in BindingDB
N/A in BindingMoad
Kd: 100000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30
  • Conformers Submitted: 10
  • Selection Criteria: structures with acceptable covalent geometry,structures with favorable non- bond energy,structures with the least restraint violations,structures with the lowest energy

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1999-11-02
  • Released Date: 2000-02-03
  • Deposition author(s): Robertson, S.A., Harada, K., Frankel, A.D., Wemmer, D.E.

Revision History

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