Research workbench
RNA kink-turn motif with pyrrolo cytosine
Analyse RNA kink-turn motif with pyrrolo cytosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EIA
- Type
- RNA
- Length
- 152 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))- R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
- Ligands
- K
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))- R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | rna | 19 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, B, C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.71 | 0.77 | 45 | K |
| 2 | 765 | 0.65 | 0.75 | 37 | K |
| 3 | 676 | 0.63 | 0.74 | 36 | empty |
| 4 | 581 | 0.61 | 0.75 | 31 | K |
| 5 | 446 | 0.57 | 0.74 | 31 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1327 Ų buried · 131 hydrogen bonds · nucleic-nucleic
- C–D · 1314 Ų buried · 126 hydrogen bonds · nucleic-nucleic
- E–F · 1314 Ų buried · 102 hydrogen bonds · nucleic-nucleic
- G–H · 1314 Ų buried · 114 hydrogen bonds · nucleic-nucleic
- C–F · 123 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 7EIA · RNA kink-turn motif with pyrrolo cytosine · 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 7EIA · PDBe 7EIA
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