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Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with threonyl sulfamoyl adenylate
Analyse Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UH0
- Type
- protein
- Length
- 420 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonyl-tRNA synthetase, mitochondrial
- EC
- 6.1.1.3
- UniProt
- P07236
- Ligands
- TSB, ZN, SO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonyl-tRNA synthetase, mitochondrial (EC 6.1.1.3) | protein | 420 | 38% helix, 23% strand | P07236 |
Ligands and binding sites
- TSB · 5'-O-(N-(L-threonyl)-sulfamoyl)adenosine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.67 | 0.81 | 40 | ZN, TSB |
| 2 | 143 | 0.43 | 0.75 | 23 | empty |
| 3 | 76 | 0.31 | 0.74 | 21 | empty |
Compared structures
- 3UH0 · Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P07236 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase, mitochondrial (P07236) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P07236
- Elsewhere: RCSB PDB 3UH0 · PDBe 3UH0 · UniProt P07236
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