Research workbench
Reverse transcriptase domain of group II intron maturase from roseburia intestinalis in P1 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
- 5IRF
- Type
- protein
- Length
- 1,142 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retron-type reverse transcriptase
- UniProt
- D4L313
- Ligands
- K
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retron-type reverse transcriptase | protein | 283 | 48% helix, 15% strand | D4L313 |
| B | Retron-type reverse transcriptase | protein | 287 | 48% helix, 16% strand | D4L313 |
| C | Retron-type reverse transcriptase | protein | 282 | 51% helix, 15% strand | D4L313 |
| D | Retron-type reverse transcriptase | protein | 290 | 50% helix, 17% strand | D4L313 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.73 | 0.78 | 84 | empty |
| 2 | 576 | 0.73 | 0.81 | 48 | empty |
| 3 | 601 | 0.73 | 0.80 | 61 | empty |
| 4 | 592 | 0.72 | 0.80 | 49 | empty |
| 5 | 544 | 0.71 | 0.80 | 51 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1708 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1613 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 357 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 304 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 136 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IRF · 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 5IRF · PDBe 5IRF · UniProt D4L313
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