1MDG

An Alternating Antiparallel Octaplex in an RNA Crystal Structure

Structural Biology Knowledgebase: 1MDG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.172

Literature

Macromolecules
Sequence Display for 1MDG

Classification: RNA

Total Structure Weight: 2271.17

Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3' A 6 synthetic

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

A COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
BGM
Query on BGM
A DNA LINKING C10 H13 Br N5 O7 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.172
  • Space Group: I 4 2 2

Unit Cell:

Length (Å) Angle (°)
a = 35.96 α = 90.00
b = 35.96 β = 90.00
c = 38.04 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2002-08-07
  • Released Date: 2003-08-12
  • Deposition author(s): Pan, B.C., Xiong, Y., Shi, K., Sundaralingam, M.

Revision History

  • 2011-09-28
    Type: Atom nomenclature | Details: fixed nomenclature errors in NCO
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4