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NMR structure of a kissing complex formed between the tar RNA element of HIV-1 and a lna modified aptamer

Analyse NMR structure of a kissing complex formed between the tar RNA element of HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PN9
Type: RNA
Length: 32 nucleotides
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'- R(*GP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*C)-3'; RNA 16-mer with locked…
Pockets: 1 · best druggability 0.66

Structure

solution nmr · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'- R(GPGPAPGPCPCPUPGPGPGPAPGPCPUPCPC)-3'	rna	16	—	—
B	RNA 16-mer with locked residues 9-10	rna	16	—	—

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	508	0.66	0.78	23	empty

Interfaces

1 interface between chains.

A–B · 411 Å² buried · 31 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

2PN9 · NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA… · 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 2PN9 · PDBe 2PN9

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