Research workbench
RNA-DNA heptamer duplex with one 2'-5'-linkage
Analyse RNA-DNA heptamer duplex with one 2'-5'-linkage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U0Q
- Type
- RNA
- Length
- 28 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3'); DNA/RNA (5'-R(*GP*GP*AP*GP*C)-D(P*T)-R(P*A)-3')
- Ligands
- MG, CO
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3') | rna | 7 | — | — |
| B, D | DNA/RNA (5'-R(*GP*GP*AP*GP*C)-D(P*T)-R(P*A)-3') | rna | 7 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- C–D · 368 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- A–B · 361 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- B–C · 90 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–D · 87 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- B–D · 83 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Compared structures
- 5U0Q · RNA-DNA heptamer duplex with one 2'-5'-linkage · 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 5U0Q · PDBe 5U0Q
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