Research workbench
X-ray analysis of a RNA tetraplex R(UGGGGU)4 at ultra-high resolution
Analyse X-ray analysis of a RNA tetraplex R(UGGGGU)4 at ultra-high resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J8G
- Type
- RNA
- Length
- 24 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*GP*GP*GP*GP*U)-3'
- Ligands
- SPM, SR, CA, NA
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 5'-R(*UP*GP*GP*GP*GP*U)-3' | rna | 6 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · chains A, B, C
- SR · Strontium ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 3 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- B–D · 324 Ų buried · 14 hydrogen bonds · nucleic-nucleic
- A–C · 321 Ų buried · 16 hydrogen bonds · nucleic-nucleic
- C–D · 57 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- B–C · 55 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–B · 29 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 1J8G · X-ray Analysis of a RNA Tetraplex r(uggggu)4 at Ultra-High Resolution · the same entry in another collection · chain C against C, 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 1J8G · PDBe 1J8G
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