Research workbench
Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the extended-duplex dimer
Analyse Solution RNA structure of loop region of the HIV-1 dimerization initiation site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D18
- Type
- RNA
- Length
- 34 nucleotides
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)- 3'
- Pockets
- 2 · best druggability 0.29
Structure
solution nmr · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)- 3' | rna | 17 | — | — |
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 | 74 | 0.29 | 0.73 | 13 | empty |
| 2 | 76 | 0.27 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 786 Ų buried · 101 hydrogen bonds · nucleic-nucleic
Compared structures
- 2D18 · Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the… · 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 2D18 · PDBe 2D18
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