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MolNFT v1 · #137268 · RNA

Guanidine-II riboswitch P2 hairpin dimer with 5-bromou substitution from pseudomonas aeruginosa

5VJB · RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)…: “Guanidine-II riboswitch P2 hairpin dimer with 5-bromou substitution from pseudomonas aeruginosa”. X-ray diffraction, 3 ligands (GAI, SPM, MG), 2 pockets (best druggability…

PDB
5VJB
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*(5BU) P*GP*C)-3')
Ligands
GAI, SPM, MG
Pockets
2 · 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*(5BU) P*GP*C)-3')rna16——

Ligands and binding sites

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

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1790.350.7713GAI
2730.250.7114empty

Interfaces

4 interfaces between chains.

  • C–D · 341 Ų buried · 21 hydrogen bonds · nucleic-nucleic
  • A–B · 338 Ų buried · 22 hydrogen bonds · nucleic-nucleic
  • B–D · 146 Ų buried · 5 hydrogen bonds · nucleic-nucleic
  • A–D · 18 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

  • 5VJB · Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas… · the same entry in another collection · chain A against A, TM-score 1.00

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