Research workbench
Crystal structure of the highly conserved RNA internal loop of srp
Analyse Crystal structure of the highly conserved RNA internal loop of srp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LNT
- Type
- RNA
- Length
- 24 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*CP*GP*UP*CP*AP*GP*GP*UP*CP*(CBV)P*G)-3'…
- Ligands
- MG, CA
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(*GP*CP*GP*UP*CP*AP*GP*GP*UP*CP*(CBV)P*G)-3' | rna | 12 | — | — |
| B | 5'-R(*CP*GP*GP*AP*AP*GP*CP*AP*GP*(CBV)P*GP*C)-3' | rna | 12 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.26 | 0.73 | 10 | CA |
Interfaces
1 interface between chains.
- A–B · 690 Ų buried · 61 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1LNT · Crystal Structure of the Highly Conserved RNA Internal Loop of SRP · 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 1LNT · PDBe 1LNT
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.