2A04

Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative

Structural Biology Knowledgebase: 2A04 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.318
  • R-Value Work: 0.254

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2A04

Classification: RNA

Total Structure Weight: 21076.63

Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3' A, C 15 synthetic
5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3' B, D 14 synthetic

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

A, C NEOMYCIN
MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN (Synonym)
C23 H46 N6 O13
PGBHMTALBVVCIT-VCIWKGPPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.318
  • R-Value Work: 0.254
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.80 α = 90.00
b = 49.90 β = 90.00
c = 144.60 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2005-06-15
  • Released Date: 2005-09-20
  • Deposition author(s): Zhao, Q., Zhao, F., Blount, K.F., Han, Q., Tor, Y., Hermann, T.

Revision History

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