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NMR structure of a kissing complex formed between the tar RNA element of HIV-1 and a LNA/RNA 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: 2OOM
Type: RNA
Length: 32 nucleotides
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA 16-mer; Tar RNA element of HIV-1
Pockets: 2 · best druggability 0.49

Structure

solution nmr · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA 16-mer	rna	16	—	—
B	Tar RNA element of HIV-1	rna	16	—	—

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	212	0.49	0.76	14	empty
2	147	0.41	0.75	11	empty

Interfaces

1 interface between chains.

A–B · 428 Å² buried · 25 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

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

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