MolNFT v1 · #120981 · protein
Reverse transcriptase domain of group II intron maturase from roseburia intestinalis in P21 space group
5HHJ · 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
- 5HHJ
- Type
- protein
- Length
- 586 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 · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retron-type reverse transcriptase | protein | 294 | 48% helix, 16% strand | D4L313 |
| B | Retron-type reverse transcriptase | protein | 292 | 47% helix, 17% strand | D4L313 |
Ligands and binding sites
- GLY · Glycine · ligand · 3 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- SIN · Succinic acid · additive · chains A
- 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.73 | 0.81 | 49 | empty |
| 2 | 516 | 0.72 | 0.81 | 46 | GLY |
| 3 | 277 | 0.56 | 0.77 | 42 | empty |
| 4 | 173 | 0.49 | 0.77 | 27 | empty |
| 5 | 92 | 0.48 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5HHJ · 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 5HHJ · PDBe 5HHJ · UniProt D4L313
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