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Structural variations and solvent structure of uggggu quadruplexes stabilized by SR2+ ions

Analyse Structural variations and solvent structure of uggggu quadruplexes stabilized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4RNE
Type
RNA
Length
48 nucleotides
Chains
8
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
Ligands
CA, SR, NA
Pockets
1 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, F, G, HRNA (5'-R(*UP*GP*GP*GP*GP*U)-3')rna6——

Ligands and binding sites

  • CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G
  • SR · Strontium ion · metal · 7 copies · chains A, B, C, D, E, F, G, H
  • NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11710.430.7513empty

Interfaces

15 interfaces between chains.

  • F–H · 323 Ų buried · 16 hydrogen bonds · nucleic-nucleic
  • E–G · 321 Ų buried · 13 hydrogen bonds · nucleic-nucleic
  • A–D · 250 Ų buried · 21 hydrogen bonds · nucleic-nucleic
  • G–H · 249 Ų buried · 19 hydrogen bonds · nucleic-nucleic
  • E–F · 248 Ų buried · 20 hydrogen bonds · nucleic-nucleic

Compared structures

  • 4RNE · Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions · the same entry in another collection · chain A against A, TM-score 1.00

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