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Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site

Analyse Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OIY
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: K, MG
Pockets: 1 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

K · Potassium ion · metal · 3 copies · chains A, B
MG · Magnesium ion · metal · 2 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	844	0.64	0.73	41	K, MG

Interfaces

1 interface between chains.

A–B · 1201 Å² buried · 100 hydrogen bonds · nucleic-nucleic

Compared structures

2OIY · Crystal structure of the duplex form of the HIV-1(LAI) 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 2OIY · PDBe 2OIY

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