Research workbench
Base pairing and structure insights into the 5-formylcytosine in RNA duplex
Analyse Base pairing and structure insights into the 5-formylcytosine in RNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HNJ
- Type
- RNA
- Length
- 48 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
- Ligands
- NA
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3') | rna | 8 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.47 | 0.73 | 17 | NA |
| 2 | 87 | 0.29 | 0.72 | 15 | empty |
Interfaces
9 interfaces between chains.
- C–D · 376 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- A–B · 373 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- E–F · 370 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- C–E · 92 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- D–F · 86 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 5HNJ · Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex · 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 5HNJ · PDBe 5HNJ
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