Research workbench
Reverse transcriptase domain of group II intron maturase from Eubacterium rectale in P21 space group
Analyse Reverse transcriptase domain of group II intron maturase from Eubacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HHL
- Type
- protein
- Length
- 2,308 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Eubacterium rectale M104/1
- Molecule
- Retron-type reverse transcriptase
- UniProt
- D4JMT6
- Ligands
- K
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.1 · 7 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retron-type reverse transcriptase | protein | 292 | 48% helix, 16% strand | D4JMT6 |
| B | Retron-type reverse transcriptase | protein | 290 | 48% helix, 17% strand | D4JMT6 |
| C, E | Retron-type reverse transcriptase | protein | 289 | 47% helix, 17% strand | D4JMT6 |
| D | Retron-type reverse transcriptase | protein | 289 | 48% helix, 16% strand | D4JMT6 |
| F | Retron-type reverse transcriptase | protein | 283 | 49% helix, 17% strand | D4JMT6 |
| G | Retron-type reverse transcriptase | protein | 289 | 49% helix, 17% strand | D4JMT6 |
| H | Retron-type reverse transcriptase | protein | 287 | 48% helix, 17% strand | D4JMT6 |
Ligands and binding sites
- K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.80 | 0.82 | 87 | empty |
| 2 | 1090 | 0.80 | 0.82 | 91 | empty |
| 3 | 1115 | 0.79 | 0.81 | 101 | empty |
| 4 | 567 | 0.73 | 0.81 | 46 | empty |
| 5 | 557 | 0.73 | 0.81 | 51 | empty |
Interfaces
16 interfaces between chains.
- C–H · 1578 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 1561 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1550 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 1527 Ų buried · 25 hydrogen bonds · protein-protein
- D–H · 670 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5HHL · Reverse transcriptase domain of group II intron maturase from eubacterium rectale in P21… · 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 D4JMT6
- Elsewhere: RCSB PDB 5HHL · PDBe 5HHL · UniProt D4JMT6
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