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Crystal structure of the HIV-1 genomic RNA dimerization initiation site

Analyse Crystal structure of the HIV-1 genomic RNA dimerization initiation site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 462D
Type: RNA
Length: 46 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (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: MG
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

MG · Magnesium ion · metal · 8 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	826	0.65	0.74	41	MG

Interfaces

1 interface between chains.

A–B · 1094 Å² buried · 108 hydrogen bonds · nucleic-nucleic

Compared structures

462D · Crystal structure of the HIV-1 genomic RNA dimerization initiation site · the same entry in another collection · chain B against B, 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 462D · PDBe 462D

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