MolNFT v1 · #27626 · RNA

HIV-1 subtype a genomic RNA dimerization initiation site

1XPF · 5'- R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP…: “HIV-1 subtype a genomic RNA dimerization initiation site”. X-ray diffraction, 4 ligands (SPM, MG, NA), 2 pockets (best druggability 0.56). MolNFT v1 #27626 on…

PDB: 1XPF
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*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP *CP*AP*AP*G)-3'
Ligands: SPM, MG, NA, SO4
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

SPM · Spermine · ligand · chains A, B
MG · Magnesium ion · metal · 3 copies · chains A, B
NA · Sodium ion · metal · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A, B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	547	0.56	0.73	34	SPM, MG
2	74	0.26	0.72	11	MG

Interfaces

1 interface between chains.

A–B · 362 Å² buried · 22 hydrogen bonds · nucleic-nucleic

Compared structures

1XPF · HIV-1 subtype A 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 1XPF · PDBe 1XPF

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