MolNFT v1 · #178727 · RNA

Crystal structure of en exoribonuclease-resistant RNA (xrrna) from potato leafroll virus (plrv)

7JJU · Potato leafroll virus xrrna: “Crystal structure of en exoribonuclease-resistant RNA (xrrna) from potato leafroll virus (plrv)”. X-ray diffraction, 2 ligands (IRI, GZ6), 4 pockets (best druggability 0.60). MolNFT v1 #178727 on…

PDB: 7JJU
Type: RNA
Length: 102 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Potato leafroll virus xrrna
Ligands: IRI, GZ6
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Potato leafroll virus xrrna	rna	51	—	—

Ligands and binding sites

IRI · Iridium hexammine ion · ligand · 10 copies · chains A, B
GZ6 · Guanidinium · ligand · 8 copies · chains A, B
CAC · Cacodylate ion · additive · 6 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	374	0.60	0.78	25	GZ6, IRI
2	399	0.60	0.77	25	GZ6
3	154	0.38	0.73	20	CAC
4	146	0.38	0.73	19	CAC

Interfaces

1 interface between chains.

A–B · 1264 Å² buried · 86 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

7JJU · Crystal structure of en exoribonuclease-resistant RNA (xrRNA) from Potato leafroll virus… · 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 7JJU · PDBe 7JJU

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