MolNFT v1 · #126045 · RNA
RNA duplex has central consecutive ga pairs flanked by G-U basepairs with a methyl group on the adenine N6
5LR4 · RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3'): “RNA duplex has central consecutive ga pairs flanked by G-U basepairs with a methyl group on the adenine N6”. X-ray diffraction, 1 ligand (NA). MolNFT v1 #126045 on GenesisL1: 3D…
- PDB
- 5LR4
- Type
- RNA
- Length
- 40 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
- Ligands
- NA
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3') | rna | 10 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- C–D · 633 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–B · 628 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- B–D · 127 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–D · 90 Ų buried · 1 hydrogen bond · nucleic-nucleic
- B–C · 89 Ų buried · 1 hydrogen bond · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 5LR4 · RNA duplex has central consecutive GA pairs flanked by G-U basepairs with a methyl group… · 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 5LR4 · PDBe 5LR4
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