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Crystal structure of a DNA-RNA chimera in complex with BA2+ ions: a case of unusual multi-domain twinning

Analyse Crystal structure of a DNA-RNA chimera in complex with BA2+ ions: a case of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5EBI
Type
RNA
Length
48 nucleotides
Chains
8
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
Ligands
BA
Pockets
2 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, F, G, HDNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')rna6——

Ligands and binding sites

  • BA · Barium ion · metal · 16 copies · chains A, E, B, H, D, G

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

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13380.520.7527BA
2520.220.7211empty

Interfaces

7 interfaces between chains.

  • A–B · 322 Ų buried · 22 hydrogen bonds · nucleic-nucleic
  • C–D · 322 Ų buried · 21 hydrogen bonds · nucleic-nucleic
  • G–H · 321 Ų buried · 23 hydrogen bonds · nucleic-nucleic
  • E–F · 320 Ų buried · 21 hydrogen bonds · nucleic-nucleic
  • A–E · 112 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

  • 5EBI · Crystal structure of a DNA-RNA chimera in complex with Ba2+ ions: a case of unusual… · the same entry in another collection · chain A against A, TM-score 1.00

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