MolNFT v1 · #103081 · RNA
Crystal structure of the tRNA-like structure from turnip yellow mosaic virus (tymv), a tRNA mimicking RNA
4P5J · Turnip yellow mosaic virus mRNA for the coat protein: “Crystal structure of the tRNA-like structure from turnip yellow mosaic virus (tymv), a tRNA mimicking RNA”. X-ray diffraction, 3 ligands (IRI, SPM, MG), 1 pocket (best…
- PDB
- 4P5J
- Type
- RNA
- Length
- 84 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Turnip yellow mosaic virus mRNA for the coat protein
- Ligands
- IRI, SPM, MG
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Turnip yellow mosaic virus mRNA for the coat protein | rna | 84 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 12 copies · chains A
- SPM · Spermine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.75 | 0.78 | 63 | MG, IRI |
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4P5J · Crystal structure of the tRNA-like structure from Turnip Yellow Mosaic Virus (TYMV), 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 4P5J · PDBe 4P5J
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