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MolNFT v1 · #120803 · RNA

RNA primer-template complex with 2-methylimidazole-activated monomer analogue-2 binding sites

5HBX · RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)…: “RNA primer-template complex with 2-methylimidazole-activated monomer analogue-2 binding sites”. X-ray diffraction, 1 ligand (PZG), 2 pockets (best druggability 0.50). MolNFT v1 #120803 on…

PDB
5HBX
Type
RNA
Length
56 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
Ligands
PZG
Pockets
2 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DRNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')rna14——

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 · 8 copies · chains A, B, C, D

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
13250.500.7320empty
23190.500.7319empty

Interfaces

2 interfaces between chains.

  • A–B · 543 Ų buried · 46 hydrogen bonds · nucleic-nucleic
  • C–D · 542 Ų buried · 43 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

  • 5HBX · RNA primer-template complex with 2-methylimidazole-activated monomer analogue-2 binding… · the same entry in another collection · chain A against A, TM-score 1.00

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