4K31

Crystal structure of apramycin bound to the leishmanial rRNA A-site

Structural Biology Knowledgebase: 4K31 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.226

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4K31

Classification: RNA / antibiotic

Total Structure Weight: 16871.21

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') B, C 23 Leishmania

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AM2
Query on AM2

B, C APRAMYCIN
NEBRAMYCIN II, 4-O-(3ALPHA-AMINO-6ALPHA-((4- AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)- 2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA- HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN- 2ALPHA-YL)-2-DEOXY-D-STREPTAMINE (Synonym)
C21 H41 N5 O11
XZNUGFQTQHRASN-XQENGBIVSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.226
  • Space Group: P 31

Unit Cell:

Length (Å) Angle (°)
a = 32.79 α = 90.00
b = 32.79 β = 90.00
c = 107.40 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2013-04-10
  • Released Date: 2013-07-31
  • Deposition author(s): Shalev, M., Kondo, J., Adir, N., Baasov, T.

Revision History

  • 2013-09-04
    Type: Citation | Details: Citation update