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MolNFT v1 · #135954 · RNA

RNA primer-template complex with guanosine dinucleotide ligand G(5') PP(5')G

5UED · RNA (5'-R(*(LCC)P*(LCC)P*(LCC) P*GP*AP*CP*UP*UP*AP*AP*GP*UP*…: “RNA primer-template complex with guanosine dinucleotide ligand G(5') PP(5')G”. X-ray diffraction, 1 ligand (86S), 1 pocket (best druggability 0.46). MolNFT v1 #135954…

PDB
5UED
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*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
Ligands
86S
Pockets
1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

  • 86S · [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R}, 3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 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
12840.460.7320empty

Interfaces

1 interface between chains.

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

Modifications

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

Compared structures

  • 5UED · RNA primer-template complex with guanosine dinucleotide ligand G(5')pp(5')G · the same entry in another collection · chain A against A, TM-score 1.00

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