Research workbench
Structure of the native tRNA-monooxygenase enzyme miae
Analyse Structure of the native tRNA-monooxygenase enzyme miae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZMB
- Type
- protein
- Length
- 399 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA hydroxylase
- UniProt
- A0A179QS89
- Ligands
- FE, CA, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | TRNA hydroxylase | protein | 199 | 74% helix, 2% strand | A0A179QS89 |
| C | TRNA hydroxylase | protein | 200 | 73% helix, 2% strand | A0A179QS89 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains B, C
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C
- PGE · Triethylene glycol · additive · 2 copies · chains C
- PG4 · Tetraethylene glycol · additive · chains B, C
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.70 | 0.89 | 34 | TRS, PG6 |
| 2 | 144 | 0.69 | 0.89 | 30 | TRS |
| 3 | 65 | 0.42 | 0.81 | 18 | empty |
| 4 | 57 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- B–C · 1073 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6ZMB · Structure of the native tRNA-Monooxygenase enzyme MiaE · the same entry in another collection · chain B against B, 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 A0A179QS89
- Elsewhere: RCSB PDB 6ZMB · PDBe 6ZMB · UniProt A0A179QS89
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