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MolNFT v1 · #118240 · RNA

Crystal structure of C9ORF72 antisense ccccgg repeat RNA associated with lou GEHRIG'S disease and frontotemporal dementia, crystallized with SR2+

5EW4 · RNA (5'- R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*…: “Crystal structure of C9ORF72 antisense ccccgg repeat RNA associated with lou GEHRIG'S disease and…”. X-ray diffraction, 4 ligands (K, MG, SR), 1 pocket (best…

PDB
5EW4
Type
RNA
Length
39 nucleotides
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'- R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)- 3')
Ligands
K, MG, SR, CL
Pockets
1 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
ARNA (5'- R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)- 3')rna19——
BRNA (5'- R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)- 3')rna20——

Ligands and binding sites

  • K · Potassium ion · metal · 9 copies · chains A, B
  • MG · Magnesium ion · metal · 2 copies · chains B
  • SR · Strontium ion · metal · chains B
  • CL · Chloride ion · ion · chains A, B

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
16330.590.7338K, MG, CL

Interfaces

1 interface between chains.

  • A–B · 865 Ų buried · 77 hydrogen bonds · nucleic-nucleic

Compared structures

  • 5EW4 · Crystal structure of C9ORF72 Antisense CCCCGG repeat RNA associated with Lou Gehrig's… · the same entry in another collection · chain A against A, TM-score 1.00

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