GL1X · GenesisL1 explorer

Research workbench

The structure of the G. violaceus guanidine II riboswitch P2 stem-loop

Analyse The structure of the G. violaceus guanidine II riboswitch P2 stem-loop in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5NDH
Type
RNA
Length
64 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*GP*(CBV) P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')
Ligands
GAI, NA, MG, SO4

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DRNA (5'-R(*GP*(CBV) P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')rna16——

Ligands and binding sites

  • GAI · Guanidine · ligand · 4 copies · chains A, B, C, D
  • NA · Sodium ion · metal · 4 copies · chains A, B, C
  • MG · Magnesium ion · metal · chains A
  • SO4 · Sulfate ion · ion · 2 copies · chains B, D

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

Interfaces

3 interfaces between chains.

  • A–C · 345 Ų buried · 21 hydrogen bonds · nucleic-nucleic
  • B–D · 338 Ų buried · 19 hydrogen bonds · nucleic-nucleic
  • B–C · 194 Ų buried · 7 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

  • 5NDH · The structure of the G. violaceus guanidine II riboswitch P2 stem-loop · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.