Research workbench
Minimal hairpin ribozyme in the transition state with G8I variation
Analyse Minimal hairpin ribozyme in the transition state with G8I variation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G6R
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Loop a substrate strand; Loop a ribozyme strand; Loop B ribozyme strand; Loop B S-turn…
- Ligands
- MG, SO4
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Loop a substrate strand | rna | 13 | — | — |
| B | Loop a ribozyme strand | rna | 12 | — | — |
| C | Loop B ribozyme strand | rna | 17 | — | — |
| D | Loop B S-turn strand | rna | 19 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.42 | 0.74 | 16 | empty |
| 2 | 167 | 0.41 | 0.74 | 20 | empty |
| 3 | 151 | 0.38 | 0.73 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 887 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–B · 639 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–D · 338 Ų buried · 6 hydrogen bonds · nucleic-nucleic
- B–C · 197 Ų buried · 9 hydrogen bonds · nucleic-nucleic
- A–C · 179 Ų buried · 7 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4G6R · Minimal Hairpin Ribozyme in the Transition State with G8I Variation · 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 4G6R · PDBe 4G6R
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