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MolNFT v1 · #46920 · RNA

Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site mn soaked

2OJ0 · 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP…: “Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site mn soaked”. X-ray diffraction, 3 ligands (K, MN, NA), 2 pockets (best…

PDB
2OJ0
Type
RNA
Length
46 nucleotides
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP *GP*CP*AP*AP*G)-3'
Ligands
K, MN, NA
Pockets
2 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP *GP*CP*AP*AP*G)-3'rna23——

Ligands and binding sites

  • K · Potassium ion · metal · 5 copies · chains A, B
  • MN · Manganese (II) ion · metal · 3 copies · chains A, B
  • NA · Sodium ion · metal · 3 copies · chains A, 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15990.590.7334K, MN, NA
2830.270.7111K, MN

Interfaces

1 interface between chains.

  • A–B · 1217 Ų buried · 107 hydrogen bonds · nucleic-nucleic

Compared structures

  • 2OJ0 · Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site… · the same entry in another collection · chain A against A, TM-score 1.00

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