1I9V

CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX

Structural Biology Knowledgebase: 1I9V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.228

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1I9V

Classification: RNA

Total Structure Weight: 25445.57

Macromolecule Entities
Molecule Chains Length Organism Details
PHENYLALANINE TRANSFER RNA A 76 Saccharomyces cerevisiae

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

A 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 MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NMY N/A in BindingDB
N/A in BindingMoad
Ki: 342000 nM  PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
YG
Query on YG
A RNA LINKING C21 H29 N6 O12 P G
5MU
Query on 5MU
A RNA LINKING C10 H15 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.228
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 54.90 α = 90.00
b = 32.90 β = 90.50
c = 63.10 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2001-03-21
  • Released Date: 2001-06-04
  • Deposition author(s): Mikkelsen, N.E., Johansson, K., Virtanen, A., Kirsebom, L.A.

Revision History

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