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MolNFT v1 · #128008 · RNA

The structure of the E.COLI guanidine II riboswitch P1 stem-loop

5NDI · RNA (5'- R(*UP*UP*UP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*CP*UP*GP*…: “The structure of the E.COLI guanidine II riboswitch P1 stem-loop”. X-ray diffraction, 2 ligands (GAI, NA), 4 pockets (best druggability 0.43). MolNFT v1 #128008 on…

PDB
5NDI
Type
RNA
Length
80 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'- R(*UP*UP*UP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*CP*UP*GP*(CBV)P*AP*AP*A)- 3')
Ligands
GAI, NA
Pockets
4 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DRNA (5'- R(*UP*UP*UP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*CP*UP*GP*(CBV)P*AP*AP*A)- 3')rna20——

Ligands and binding sites

  • GAI · Guanidine · ligand · 4 copies · chains A, B, C, D
  • NA · Sodium ion · metal · chains A, B

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12150.430.7316empty
22000.430.7417empty
31750.400.7317empty
41520.370.7217empty

Interfaces

3 interfaces between chains.

  • A–B · 335 Ų buried · 21 hydrogen bonds · nucleic-nucleic
  • C–D · 325 Ų buried · 20 hydrogen bonds · nucleic-nucleic
  • A–C · 84 Ų buried · 3 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

  • 5NDI · The structure of the E.coli guanidine II riboswitch P1 stem-loop · the same entry in another collection · chain A against A, TM-score 1.00

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