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The crystal structure of a D-lysine-based chiral pna-DNA duplex

Analyse The crystal structure of a D-lysine-based chiral pna-DNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1NR8
Type
DNA
Length
10 nucleotides
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(P*AP*GP*TP*GP*AP*TP*CP*TP*AP*C)-3'
Ligands
GPN, TPN, APN, A66, T66, C66, CPN, MG, NH2

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A5'-D(P*AP*GP*TP*GP*AP*TP*CP*TP*AP*C)-3'dna10——

Ligands and binding sites

  • GPN · 2-aminoethylglycine-carbonylmethylene-guanine · ligand · 2 copies · chains A
  • TPN · 2-aminoethylglycine-carbonylmethylene-thymine · ligand · 2 copies · chains A
  • APN · 2-aminoethylglycine-carbonylmethylene-adenine · ligand · 2 copies · chains A
  • A66 · 2-aminoethyllysine-carbonylmethylene-adenine · ligand · chains A
  • T66 · 2-aminoethyllysine-carbonylmethylene-thymine · ligand · chains A
  • C66 · 2-aminoethyllysine-carbonylmethylene-cytosine · ligand · chains A
  • CPN · 2-aminoethylglycine-carbonylmethylene-cytosine · ligand · chains A
  • MG · Magnesium ion · metal · chains A
  • NH2 · Amino group · ion

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

  • 1NR8 · The crystal structure of a D-Lysine-based chiral PNA-DNA duplex · the same entry in another collection · chain A against A, TM-score 1.00

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