Research workbench
Structure of the tRNA-monooxygenase enzyme miae frozen under 140 bar of krypton using the soak and freeze methodology
Analyse Structure of the tRNA-monooxygenase enzyme miae frozen under 140 bar of krypton… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZMA
- Type
- protein
- Length
- 398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA hydroxylase
- UniProt
- A0A179QS89
- Ligands
- FE, CA, KR, CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | TRNA hydroxylase | protein | 199 | 73% helix, 1% strand | A0A179QS89 |
| C | TRNA hydroxylase | protein | 199 | 73% helix, 1% strand | A0A179QS89 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains B, C
- CA · Calcium ion · metal · 2 copies · chains B
- KR · Krypton · ion · 6 copies · chains B, C
- CL · Chloride ion · ion · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, C
- PG4 · Tetraethylene glycol · additive · chains B, 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 | 165 | 0.71 | 0.89 | 32 | TRS, PEG, KR |
| 2 | 192 | 0.71 | 0.88 | 36 | TRS, PEG, KR |
| 3 | 65 | 0.41 | 0.80 | 17 | empty |
| 4 | 54 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- B–C · 1057 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6ZMA · Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 140 bar of krypton using the… · 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 6ZMA · PDBe 6ZMA · UniProt A0A179QS89
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