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Solution RNA structure model of the HIV-1 dimerization initiation site in the extended-duplex dimer

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

PDB: 2D1A
Type: RNA
Length: 78 nucleotides
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA
Pockets: 2 · best druggability 0.52

Structure

solution nmr · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA	rna	39	—	—

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	405	0.52	0.73	30	empty
2	270	0.47	0.73	23	empty

Interfaces

1 interface between chains.

A–B · 1806 Å² buried · 230 hydrogen bonds · nucleic-nucleic

Compared structures

2D1A · Solution RNA structure model of the HIV-1 dimerization initiation site in the… · 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 2D1A · PDBe 2D1A

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