MolNFT v1 · #126035 · RNA
RNA duplex has central consecutive ga pairs flanked by G-C basepairs
5LQT · RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*CP*GP*GP*C)-3'): “RNA duplex has central consecutive ga pairs flanked by G-C basepairs”. X-ray diffraction, 3 ligands (MG, CA, NA), 1 pocket (best druggability 0.26). MolNFT v1 #126035 on…
- PDB
- 5LQT
- Type
- RNA
- Length
- 20 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*CP*GP*GP*C)-3')
- Ligands
- MG, CA, NA
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*CP*GP*GP*C)-3') | rna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · 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 | 75 | 0.26 | 0.72 | 13 | MG |
Interfaces
1 interface between chains.
- A–B · 486 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5LQT · RNA duplex has central consecutive GA pairs flanked by G-C basepairs · 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 5LQT · PDBe 5LQT
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