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MolNFT v1 · #121161 · RNA

Base pairing and structure insights into the 5-formylcytosine in RNA duplex

5HN2 · RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3'): “Base pairing and structure insights into the 5-formylcytosine in RNA duplex”. X-ray diffraction, 1 ligand (NA), 1 pocket (best druggability 0.78). MolNFT v1 #121161 on GenesisL1: 3D…

PDB
5HN2
Type
RNA
Length
48 nucleotides
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
Ligands
NA
Pockets
1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, FRNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')rna8——

Ligands and binding sites

  • NA · Sodium ion · metal · chains E, F

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11150.780.9814empty

Interfaces

12 interfaces between chains.

  • A–B · 375 Ų buried · 32 hydrogen bonds · nucleic-nucleic
  • E–F · 370 Ų buried · 33 hydrogen bonds · nucleic-nucleic
  • C–D · 369 Ų buried · 28 hydrogen bonds · nucleic-nucleic
  • C–F · 119 Ų buried · 1 hydrogen bond · nucleic-nucleic
  • B–E · 114 Ų buried · 2 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 6 modified (nucleotide modification).

Compared structures

  • 5HN2 · Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex · the same entry in another collection · chain A against A, TM-score 1.00

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