MolNFT v1 · #27625 · RNA

HIV-1 subtype B genomic RNA dimerization initiation site

1XPE · 5'- R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP…: “HIV-1 subtype B genomic RNA dimerization initiation site”. X-ray diffraction, 4 ligands (NA, MG, SO4), 1 pocket (best druggability 0.63). MolNFT v1 #27625 on GenesisL1…

PDB: 1XPE
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: NA, MG, SO4, CL
Pockets: 1 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'- R(CPUPUPGPCPUPGPAPAPGPCPGPCPGPCPAPCPGPGP CPAPAP*G)-3'	rna	23	—	—

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A
SO4 · Sulfate ion · ion · 4 copies · chains A, B
CL · Chloride ion · ion · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	807	0.63	0.73	42	MG, CL

Interfaces

1 interface between chains.

A–B · 376 Å² buried · 38 hydrogen bonds · nucleic-nucleic

Compared structures

1XPE · HIV-1 subtype B genomic RNA Dimerization Initiation Site · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1XPE · PDBe 1XPE

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.