Research workbench
RNA hairpin containing gpppg-oligo to mimic intermediate formed by activated monomer and activated downstream helper
Analyse RNA hairpin containing gpppg-oligo to mimic intermediate formed by activated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BMD
- Type
- RNA
- Length
- 93 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC) P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*…
- Ligands
- GP3
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC) P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3') | rna | 24 | — | — |
| B, D, F | RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3') | rna | 7 | — | — |
Ligands and binding sites
- GP3 · Diguanosine-5'-triphosphate · ligand · 3 copies · chains A, B, D, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 150 | 0.36 | 0.72 | 13 | empty |
| 2 | 108 | 0.30 | 0.72 | 10 | empty |
Interfaces
7 interfaces between chains.
- C–E · 380 Ų buried · 9 hydrogen bonds · nucleic-nucleic
- C–D · 312 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- A–B · 308 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- E–F · 305 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- D–E · 153 Ų buried · 7 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified, 3 covalent (nucleotide modification, covalent ligand).
Compared structures
- 6BMD · RNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer and… · 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 6BMD · PDBe 6BMD
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