Research workbench
Reverse transcriptase domain of group II intron maturase from roseburia intestinalis in P21 space group
Analyse Reverse transcriptase domain of group II intron maturase from roseburia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HHJ
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retron-type reverse transcriptase
- UniProt
- D4L313
- Ligands
- GLY, K, PO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retron-type reverse transcriptase | protein | 294 | 48% helix, 16% strand | D4L313 |
| B | Retron-type reverse transcriptase | protein | 292 | 47% helix, 17% strand | D4L313 |
Ligands and binding sites
- GLY · Glycine · ligand · 3 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- SIN · Succinic acid · additive · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.73 | 0.81 | 49 | empty |
| 2 | 516 | 0.72 | 0.81 | 46 | GLY |
| 3 | 277 | 0.56 | 0.77 | 42 | empty |
| 4 | 173 | 0.49 | 0.77 | 27 | empty |
| 5 | 92 | 0.48 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5HHJ · Reverse transcriptase domain of group II intron maturase from Roseburia intestinalis in… · 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 D4L313
- Elsewhere: RCSB PDB 5HHJ · PDBe 5HHJ · UniProt D4L313
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.