Research workbench
Crystal structure of en exoribonuclease-resistant RNA (xrrna) from potato leafroll virus (plrv)
Analyse Crystal structure of en exoribonuclease-resistant RNA (xrrna) from potato… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų 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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