MolNFT v1 · #84965 · RNA
Octamer 5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3' with six watson-crick base-pairs and two 3' overhang residues
419D · DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3'): “Octamer 5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3' with six watson-crick base-pairs and two 3' overhang residues”. X-ray diffraction, 1 pocket (best druggability 0.54). MolNFT v1 #84965 on…
- PDB
- 419D
- Type
- RNA
- Length
- 32 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3') | rna | 8 | — | — |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.54 | 0.77 | 22 | empty |
Interfaces
4 interfaces between chains.
- C–D · 310 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- A–B · 283 Ų buried · 20 hydrogen bonds · nucleic-nucleic
- B–D · 173 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–C · 86 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 419D · Octamer 5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3' with six watson-crick base-pairs and two 3'… · 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 419D · PDBe 419D
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