1DDY

MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER

Structural Biology Knowledgebase: 1DDY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1DDY

Classification: RNA

Total Structure Weight: 50569.31

Macromolecule Entities
Molecule Chains Length Organism Details
VITAMIN B12 BINDING RNA A, C, E, G 35 synthetic COMPLEXED WITH COBALAMIN, VITAMIN B12

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B12
Query on B12

A, C, E, G COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NME
Query on NME

A, C, E, G METHYLAMINE
C H5 N
BAVYZALUXZFZLV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.204
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 91.33 α = 90.00
b = 161.88 β = 90.00
c = 100.96 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1999-11-12
  • Released Date: 2000-01-01
  • Deposition author(s): Sussman, D., Nix, J.C., Wilson, C.

Revision History

  • 2012-10-24
    Type: Non-polymer description | Details: --
  • 2011-12-28
    Type: Advisory | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4