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Guanidine-II riboswitch P2 hairpin dimer from pseudomonas aeruginosa

Analyse Guanidine-II riboswitch P2 hairpin dimer from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5VJ9
Type
RNA
Length
64 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)- 3')
Ligands
SPM, GAI, MG, K
Pockets
1 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

  • SPM · Spermine · ligand · 5 copies · chains A, B, C, D
  • GAI · Guanidine · ligand · 4 copies · chains A, B, C, D
  • MG · Magnesium ion · metal · chains B
  • K · Potassium ion · metal · chains D

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
1850.350.7613GAI

Interfaces

4 interfaces between chains.

  • C–D · 343 Ų buried · 21 hydrogen bonds · nucleic-nucleic
  • A–B · 343 Ų buried · 25 hydrogen bonds · nucleic-nucleic
  • B–D · 150 Ų buried · 6 hydrogen bonds · nucleic-nucleic
  • A–D · 16 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

  • 5VJ9 · Guanidine-II riboswitch P2 hairpin dimer from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00

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