Research workbench
Cryo-EM structure of a pre-catalytic group II intron rnp
Analyse Cryo-EM structure of a pre-catalytic group II intron rnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D0F
- Type
- protein + RNA
- Length
- 1,185 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (738-mer); Group II intron-encoded protein ltra
- EC
- 2.7.7.49, 3.1.-.-
- UniProt
- P0A3U0
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 36% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (738-mer) | rna | 738 | — | — |
| C | Group II intron-encoded protein ltra (EC 2.7.7.49, 3.1.-.-) | protein | 447 | 36% helix, 4% strand | P0A3U0 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.87 | 0.88 | 129 | empty |
| 2 | 912 | 0.80 | 0.83 | 102 | empty |
| 3 | 487 | 0.74 | 0.84 | 40 | empty |
| 4 | 320 | 0.73 | 0.86 | 40 | empty |
| 5 | 1069 | 0.73 | 0.78 | 50 | empty |
Interfaces
1 interface between chains.
- A–C · 3089 Ų buried · 98 hydrogen bonds · protein-nucleic
Compared structures
- 7D0F · cryo-EM structure of a pre-catalytic group II intron RNP · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3U0 · AlphaFold monomer V2.0 prediction for group II intron-encoded protein ltra (P0A3U0) · a predicted model of the same protein · chain C against A, TM-score 0.75
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A3U0
- Elsewhere: RCSB PDB 7D0F · PDBe 7D0F · UniProt P0A3U0
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