Research workbench
Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase - orthorhombic crystal form
Analyse Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UGT
- Type
- protein
- Length
- 1,683 residues
- Chains
- 4
- 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
- ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonyl-tRNA synthetase, mitochondrial (EC 6.1.1.3) | protein | 419 | 37% helix, 20% strand | P07236 |
| B | Threonyl-tRNA synthetase, mitochondrial (EC 6.1.1.3) | protein | 419 | 35% helix, 18% strand | P07236 |
| C | Threonyl-tRNA synthetase, mitochondrial (EC 6.1.1.3) | protein | 427 | 33% helix, 21% strand | P07236 |
| D | Threonyl-tRNA synthetase, mitochondrial (EC 6.1.1.3) | protein | 418 | 33% helix, 21% strand | P07236 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.89 | 0.90 | 83 | empty |
| 2 | 1101 | 0.88 | 0.89 | 92 | empty |
| 3 | 1056 | 0.75 | 0.77 | 78 | empty |
| 4 | 162 | 0.66 | 0.86 | 31 | empty |
| 5 | 55 | 0.66 | 0.95 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3646 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3588 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 905 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3UGT · Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase - orthorhombic… · the same entry in another collection · chain D against D, TM-score 1.00
- P07236 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase, mitochondrial (P07236) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 3UGT · PDBe 3UGT · UniProt P07236
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