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MolNFT v1 · #13785 · RNA

Crystal structure of the highly conserved RNA internal loop of srp

1LNT · 5'-R(*GP*CP*GP*UP*CP*AP*GP*GP*UP*CP*(CBV)P*G)-3': “Crystal structure of the highly conserved RNA internal loop of srp”. X-ray diffraction, 2 ligands (MG, CA), 1 pocket (best druggability 0.26). MolNFT v1 #13785 on GenesisL1: 3D…

PDB
1LNT
Type
RNA
Length
24 nucleotides
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-R(*GP*CP*GP*UP*CP*AP*GP*GP*UP*CP*(CBV)P*G)-3'…
Ligands
MG, CA
Pockets
1 · best druggability 0.26

Structure

x-ray diffraction · 2 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A5'-R(*GP*CP*GP*UP*CP*AP*GP*GP*UP*CP*(CBV)P*G)-3'rna12——
B5'-R(*CP*GP*GP*AP*AP*GP*CP*AP*GP*(CBV)P*GP*C)-3'rna12——

Ligands and binding sites

  • MG · Magnesium ion · metal · 4 copies · chains A, B
  • CA · Calcium ion · metal · 3 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
1590.260.7310CA

Interfaces

1 interface between chains.

  • A–B · 690 Ų buried · 61 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

  • 1LNT · Crystal Structure of the Highly Conserved RNA Internal Loop of SRP · the same entry in another collection · chain A against A, TM-score 1.00

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