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Crystal structure of HIV-1 subtype F dis extended duplex RNA bound to ribostamycin (U267OME)

Analyse Crystal structure of HIV-1 subtype F dis extended duplex RNA bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DVV
Type: RNA
Length: 46 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 genomic RNA
Ligands: RIO, K, CL
Pockets: 1 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 genomic RNA	rna	23	—	—

Ligands and binding sites

RIO · Ribostamycin · ligand · 2 copies · chains A, B
K · Potassium ion · metal · 4 copies · chains A, B
CL · Chloride ion · ion · chains A

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	1037	0.68	0.74	43	RIO, K, CL

Interfaces

1 interface between chains.

A–B · 1254 Å² buried · 109 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3DVV · Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin… · 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 3DVV · PDBe 3DVV

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