Research workbench
RNA kink-turn motif with 2-aminopurine
Analyse RNA kink-turn motif with 2-aminopurine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EI7
- Type
- RNA
- Length
- 38 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))- R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
- Ligands
- CO
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))- R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | rna | 19 | — | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 515 | 0.58 | 0.74 | 28 | CO |
Interfaces
1 interface between chains.
- A–B · 1305 Ų buried · 133 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7EI7 · RNA kink-turn motif with 2-aminopurine · 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 7EI7 · PDBe 7EI7
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