MolNFT v1 · #177427 · RNA
RNA kink-turn motif with 2-aminopurine
7EI8 · RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))…: “RNA kink-turn motif with 2-aminopurine”. X-ray diffraction, 1 ligand (CO), 1 pocket (best druggability 0.66). MolNFT v1 #177427 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7EI8
- Type
- RNA
- Length
- 76 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))…
- Ligands
- CO
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))- R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | rna | 19 | — | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 14 copies · chains A, B, C, D
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 | 1165 | 0.66 | 0.73 | 59 | CO |
Interfaces
6 interfaces between chains.
- C–D · 1320 Ų buried · 110 hydrogen bonds · nucleic-nucleic
- A–B · 1289 Ų buried · 110 hydrogen bonds · nucleic-nucleic
- A–D · 165 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–C · 160 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- B–D · 89 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 16 modified (nucleotide modification).
Compared structures
- 7EI8 · 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 7EI8 · PDBe 7EI8
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