MolNFT v1 · #120982 · protein
Reverse transcriptase domain of group II intron maturase from roseburia intestinalis in P21 space group (se-met)
5HHK · Retron-type reverse transcriptase: “Reverse transcriptase domain of group II intron maturase from roseburia intestinalis in P21 space group…”. X-ray diffraction, 3 ligands (GLY, K, PO4), 7 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5HHK
- Type
- protein
- Length
- 582 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 · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retron-type reverse transcriptase | protein | 293 | 48% helix, 17% strand | D4L313 |
| B | Retron-type reverse transcriptase | protein | 289 | 49% helix, 17% strand | D4L313 |
Ligands and binding sites
- GLY · Glycine · ligand · 4 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.73 | 0.81 | 47 | empty |
| 2 | 523 | 0.72 | 0.81 | 49 | GLY |
| 3 | 279 | 0.57 | 0.77 | 44 | empty |
| 4 | 211 | 0.52 | 0.77 | 31 | empty |
| 5 | 101 | 0.47 | 0.80 | 23 | GLY |
Interfaces
1 interface between chains.
- A–B · 1684 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 5HHK · 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 5HHK · PDBe 5HHK · UniProt D4L313
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