1NR8

The crystal structure of a D-Lysine-based chiral PNA-DNA duplex

Structural Biology Knowledgebase: 1NR8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NR8

Classification: DNA / PEPTIDE NUCLEIC ACID

Total Structure Weight: 6014.40

Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(P*AP*GP*TP*GP*AP*TP*CP*TP*AP*C)-3' A 10 synthetic DNA
H-((GPN)*(TPN)*(APN)*(GPN)*(A66)*(T66)*(C66)*(APN)*(CPN)*(TPN))-NH2 B 11 synthetic peptide nucleic acid

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

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 8 Unique
ID Chains Type Formula 2D Diagram Parent
GPN
Query on GPN
B PEPTIDE-LIKE C11 H16 N7 O4 --
TPN
Query on TPN
B PEPTIDE-LIKE C11 H17 N4 O5 --
APN
Query on APN
B PEPTIDE-LIKE C11 H16 N7 O3 --
A66
Query on A66
B L-PEPTIDE LINKING C15 H24 N8 O3 --
T66
Query on T66
B L-PEPTIDE LINKING C15 H25 N5 O5 --
C66
Query on C66
B L-PEPTIDE LINKING C14 H24 N6 O4 --
CPN
Query on CPN
B PEPTIDE-LIKE C10 H16 N5 O4 --
NH2
Query on NH2
B NON-POLYMER H2 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197
  • Space Group: P 31
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 34.94 α = 90.00
b = 34.94 β = 90.00
c = 35.80 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2003-01-24
  • Released Date: 2003-10-28
  • Deposition author(s): Menchise, V., De Simone, G., Tedeschi, T., Corradini, R., Sforza, S., Marchelli, R., Capasso, D., Saviano, M., Pedone, C.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4