MolNFT v1 · #81105 · protein
Crystal structure of the apo form of the yeast mitochondrial threonyl- tRNA synthetase determined at 2.1 ångström resolution
3UGQ · Threonyl-tRNA synthetase, mitochondrial: “Crystal structure of the apo form of the yeast mitochondrial threonyl- tRNA synthetase determined at 2.1…”. X-ray diffraction, 3 ligands (K, ZN, SO4), 4 pockets (best druggability 0.65).…
- PDB
- 3UGQ
- Type
- protein
- Length
- 426 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
- K, ZN, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonyl-tRNA synthetase, mitochondrial (EC 6.1.1.3) | protein | 426 | 37% helix, 24% strand | P07236 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.65 | 0.81 | 43 | SO4, K |
| 2 | 162 | 0.44 | 0.75 | 23 | empty |
| 3 | 53 | 0.35 | 0.79 | 15 | empty |
| 4 | 62 | 0.29 | 0.74 | 20 | empty |
Compared structures
- 3UGQ · Crystal structure of the apo form of the yeast mitochondrial threonyl-tRNA synthetase… · 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 3UGQ · PDBe 3UGQ · UniProt P07236
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