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MolNFT v1 · #16250 · RNA

2.9 a crystal structure of streptomycin RNA-aptamer

1NTA · 5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP…: “2.9 a crystal structure of streptomycin RNA-aptamer”. X-ray diffraction, 3 ligands (SRY, BA, NA), 1 pocket (best druggability 0.52). MolNFT v1 #16250 on GenesisL1: 3D…

PDB
1NTA
Type
RNA
Length
40 nucleotides
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP *UP*GP*CP*C)-3'…
Ligands
SRY, BA, NA
Pockets
1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP *UP*GP*CP*C)-3'rna22——
B5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C) -3'rna18——

Ligands and binding sites

  • SRY · Streptomycin · ligand · chains A, B
  • BA · Barium ion · metal · 3 copies · chains A, B
  • NA · Sodium 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12600.520.7626BA, SRY

Interfaces

1 interface between chains.

  • A–B · 1089 Ų buried · 92 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1NTA · 2.9 A crystal structure of Streptomycin RNA-aptamer · the same entry in another collection · chain A against A, TM-score 1.00

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