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The crystal structure of a DNA:RNA hybrid duplex sequence cttttctttg containing an lna-amide-lna modification

Analyse The crystal structure of a DNA:RNA hybrid duplex sequence cttttctttg containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7OOO
Type
DNA + RNA
Length
38 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'); DNA…
Ligands
MG

Structure

x-ray diffraction · 2 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, DRNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')rna10——
B, EDNA (5'-D(*CP*TP*(RWQ)P*TP*CP*TP*TP*TP*G)-3')dna9——

Ligands and binding sites

  • MG · Magnesium ion · metal · 2 copies · chains B, D

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

Interfaces

6 interfaces between chains.

  • A–B · 488 Ų buried · 48 hydrogen bonds · nucleic-nucleic
  • D–E · 487 Ų buried · 48 hydrogen bonds · nucleic-nucleic
  • B–D · 146 Ų buried · 2 hydrogen bonds · nucleic-nucleic
  • A–E · 136 Ų buried · 2 hydrogen bonds · nucleic-nucleic
  • A–D · 122 Ų buried · 7 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

  • 7OOO · The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG containing an… · the same entry in another collection · chain A against A, TM-score 1.00

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