Research workbench
Crystal structure of helix II of the X. laevis somatic 5S rRNA with a cytosine bulge in two conformations
Analyse Crystal structure of helix II of the X. laevis somatic 5S rRNA with a cytosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DQF
- Type
- RNA
- Length
- 19 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)-3'); RNA (5'-R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3')
- Ligands
- CA
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)-3') | rna | 9 | — | — |
| B | RNA (5'-R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3') | rna | 10 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Compared structures
- 1DQF · Crystal structure of helix II of the X. laevis somatic 5S rRNA with a cytosine bulge in… · 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 1DQF · PDBe 1DQF
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.