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MolNFT v1 · #165867 · RNA

RNA duplex bound with tna 3'-3' imidazolium dimer

6U8U · RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)…: “RNA duplex bound with tna 3'-3' imidazolium dimer”. X-ray diffraction, 2 ligands (Q1V, MG), 1 pocket (best druggability 0.47). MolNFT v1 #165867 on GenesisL1: 3D structure, binding sites and…

PDB
6U8U
Type
RNA
Length
28 nucleotides
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
Ligands
Q1V, MG
Pockets
1 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')rna14——

Ligands and binding sites

  • Q1V · 2-amino-3-[(R)-{[(3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-hydroxyoxolan-3-yl]oxy}(hydroxy)phosphoryl]-1-[(S)-{[(3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-hydroxyoxolan-3-yl]oxy}(hydroxy)phosphoryl]-1H-imidazol-3-ium · ligand · 2 copies · chains A, B
  • MG · Magnesium ion · metal · 2 copies · chains A, B

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
13080.470.7219MG

Interfaces

1 interface between chains.

  • A–B · 580 Ų buried · 48 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 modified (nucleotide modification).

Compared structures

  • 6U8U · RNA duplex bound with TNA 3'-3' imidazolium dimer · the same entry in another collection · chain A against A, TM-score 1.00

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