MolNFT v1 · #156742 · protein + DNA + RNA
Structure of a group II intron retroelement prior to DNA integration
6ME0 · T.EL4H RNA: “Structure of a group II intron retroelement prior to DNA integration”. Electron microscopy, 2 ligands (MG, NA), 20 pockets (best druggability 0.81). MolNFT v1 #156742 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ME0
- Type
- protein + DNA + RNA
- Length
- 1,259 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 0.81
Structure
electron microscopy · 3 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T.EL4H RNA | rna | 829 | — | — |
| B | Sense target DNA | dna | 16 | — | — |
| C | Maturase reverse transcriptase | protein | 414 | 47% helix, 11% 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 | 783 | 0.81 | 0.85 | 60 | MG |
| 2 | 769 | 0.75 | 0.80 | 53 | empty |
| 3 | 423 | 0.73 | 0.84 | 30 | empty |
| 4 | 699 | 0.72 | 0.79 | 57 | empty |
| 5 | 67 | 0.70 | 0.96 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3814 Ų buried · 80 hydrogen bonds · protein-nucleic
- A–B · 1181 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- B–C · 1142 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6ME0 · Structure of a group II intron retroelement prior to 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 6ME0 · PDBe 6ME0 · UniProt Q8DMK2
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