MolNFT v1 · #122514 · protein
Reverse transcriptase domain of group II intron maturase from roseburia intestinalis in P212121 space group
5IRG · Retron-type reverse transcriptase: “Reverse transcriptase domain of group II intron maturase from roseburia intestinalis in P212121 space group”. X-ray diffraction, 1 ligand (K), 14 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5IRG
- Type
- protein
- Length
- 1,145 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
- 14 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retron-type reverse transcriptase | protein | 287 | 48% helix, 17% strand | D4L313 |
| B | Retron-type reverse transcriptase | protein | 288 | 48% helix, 17% strand | D4L313 |
| C | Retron-type reverse transcriptase | protein | 284 | 49% helix, 16% strand | D4L313 |
| D | Retron-type reverse transcriptase | protein | 286 | 48% helix, 16% 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.77 | 0.79 | 88 | empty |
| 2 | 602 | 0.73 | 0.81 | 54 | empty |
| 3 | 562 | 0.72 | 0.81 | 54 | empty |
| 4 | 520 | 0.72 | 0.81 | 45 | empty |
| 5 | 565 | 0.70 | 0.79 | 49 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1792 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1744 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 541 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 340 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 5IRG · 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 5IRG · PDBe 5IRG · UniProt D4L313
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