Research workbench
Structure of a group II intron retroelement after DNA integration
Analyse Structure of a group II intron retroelement after DNA integration in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MEC
- Type
- protein + DNA + RNA
- Length
- 1,246 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T.EL4H RNA; Sense target DNA; Maturase reverse transcriptase
- UniProt
- Q8DMK2
- Ligands
- MG, NA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T.EL4H RNA | rna | 818 | — | — |
| B | Sense target DNA | dna | 14 | — | — |
| C | Maturase reverse transcriptase | protein | 414 | 46% helix, 10% strand | Q8DMK2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 854 | 0.79 | 0.83 | 62 | MG |
| 2 | 1043 | 0.78 | 0.81 | 62 | MG |
| 3 | 866 | 0.77 | 0.81 | 65 | MG |
| 4 | 719 | 0.74 | 0.80 | 55 | empty |
| 5 | 817 | 0.73 | 0.79 | 46 | MG |
Interfaces
3 interfaces between chains.
- A–C · 4261 Ų buried · 101 hydrogen bonds · protein-nucleic
- B–C · 1078 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 1016 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 6MEC · Structure of a group II intron retroelement after DNA integration · 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
- Every structure of UniProt Q8DMK2
- Elsewhere: RCSB PDB 6MEC · PDBe 6MEC · UniProt Q8DMK2
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