GL1X · GenesisL1 explorer

MolNFT v1 · #174245 · RNA

Structure of L-threoninol nucleic acid - RNA complex

7BPF · RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3'): “Structure of L-threoninol nucleic acid - RNA complex”. X-ray diffraction, 4 ligands (F6X, F73, F6U). MolNFT v1 #174245 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7BPF
Type
RNA
Length
14 nucleotides
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
Ligands
F6X, F73, F6U, GT3

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BRNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')rna7——

Ligands and binding sites

  • F6X · [(2R,3R)-3-[2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] dihydrogen phosphate · ligand · 6 copies · chains A, B
  • F73 · [(2R,3R)-3-[2-(2-azanyl-6-oxidanylidene-1H-purin-9-yl) ethanoylamino]-4-oxidanyl-butan-2-yl] dihydrogen phosphate · ligand · 4 copies · chains A, B
  • F6U · [(2R,3R)-3-[2-(6-aminopurin-9-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] dihydrogen phosphate · ligand · 4 copies · chains A, B
  • GT3 · 2-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-N-[(2R,3R)-1,3-bis(oxidanyl)butan-2-yl]ethanamide · ligand · 2 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

  • A–B · 116 Ų buried · 4 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

  • 7BPF · Structure of L-threoninol nucleic acid - RNA complex · the same entry in another collection · chain A against A, TM-score 1.00

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