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MolNFT v1 · #124851 · RNA

RNA 15MER duplex binding with pzg monomer

5KRG · RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)…: “RNA 15MER duplex binding with pzg monomer”. X-ray diffraction, 1 ligand (PZG), 2 pockets (best druggability 0.47). MolNFT v1 #124851 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
5KRG
Type
RNA
Length
60 nucleotides
Chains
4
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*GP*G)-3')
Ligands
PZG
Pockets
2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3')rna15——

Ligands and binding sites

  • PZG · [(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-(3-methyl-1~{H}-pyrazol-4-yl)phosphinic acid · ligand · 4 copies · chains A, C, D, 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
13050.470.7321empty
22380.430.7218empty

Interfaces

3 interfaces between chains.

  • C–D · 694 Ų buried · 59 hydrogen bonds · nucleic-nucleic
  • A–B · 693 Ų buried · 57 hydrogen bonds · nucleic-nucleic
  • A–C · 66 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 16 modified (nucleotide modification).

Compared structures

  • 5KRG · RNA 15mer duplex binding with PZG monomer · the same entry in another collection · chain A against A, TM-score 1.00

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