MolNFT v1 · #122513 · protein
Reverse transcriptase domain of group II intron maturase from roseburia intestinalis in P1 space group
5IRF · Retron-type reverse transcriptase: “Reverse transcriptase domain of group II intron maturase from roseburia intestinalis in P1 space group”. X-ray diffraction, 1 ligand (K), 13 pockets (best druggability 0.73). MolNFT v1 #122513 on…
- 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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