Research workbench
Crystal structure of 2-selenouridine containing RNA
Analyse Crystal structure of 2-selenouridine containing RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JAH
- Type
- RNA
- Length
- 48 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*UP*GP*UP*AP*(RUS)P*AP*C)-3')
- Ligands
- K
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, C, F | RNA (5'-R(*GP*UP*GP*UP*AP*(RUS)P*AP*C)-3') | rna | 8 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.76 | 0.97 | 13 | empty |
| 2 | 138 | 0.37 | 0.74 | 12 | empty |
| 3 | 94 | 0.30 | 0.72 | 12 | empty |
Interfaces
12 interfaces between chains.
- D–C · 283 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- A–B · 281 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- E–F · 276 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- A–D · 123 Ų buried · 1 hydrogen bond · nucleic-nucleic
- C–F · 119 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 4JAH · Crystal structure of 2-Selenouridine containing RNA · 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 4JAH · PDBe 4JAH
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