Research workbench
Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the second-step self-splicing
Analyse Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YGA
- Type
- RNA
- Length
- 407 nucleotides
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Tetrahymena; SYNTHETIC CONSTRUCT
- Molecule
- RNA (5'-R(*UP*CP*GP*(SSU)P*AP*AP*CP*C)-3'); RNA (5'-R(*CP*CP*CP*UP*CP*U)-3'); RNA…
- Ligands
- MG
- Pockets
- 18 · best druggability 0.72
Structure
electron microscopy · resolution 2.35 · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (5'-R(*UP*CP*GP*(SSU)P*AP*AP*CP*C)-3') | rna | 8 | — | — |
| B | RNA (5'-R(*CP*CP*CP*UP*CP*U)-3') | rna | 6 | — | — |
| N | RNA (393-mer) | rna | 393 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.72 | 0.77 | 56 | MG |
| 2 | 139 | 0.70 | 0.92 | 19 | MG |
| 3 | 581 | 0.69 | 0.79 | 32 | empty |
| 4 | 464 | 0.66 | 0.79 | 47 | MG |
| 5 | 548 | 0.64 | 0.77 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–N · 776 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- B–N · 459 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- A–B · 104 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7YGA · PDBe 7YGA
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