Research workbench
Crystal structure of the editing domain of threonyl-tRNA synthetase from pyrococcus abyssi in complex with an analog of threonyl- adenylate
Analyse Crystal structure of the editing domain of threonyl-tRNA synthetase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PD5
- Type
- protein
- Length
- 289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonyl-tRNA synthetase
- EC
- 6.1.1.3
- UniProt
- Q9UZ14
- Ligands
- TSB
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 142 | 31% helix, 39% strand | Q9UZ14 |
| B | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 147 | 29% helix, 38% strand | Q9UZ14 |
Ligands and binding sites
- TSB · 5'-O-(N-(L-threonyl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.74 | 0.98 | 12 | empty |
| 2 | 209 | 0.62 | 0.82 | 29 | TSB |
| 3 | 182 | 0.61 | 0.82 | 25 | TSB |
| 4 | 51 | 0.23 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1151 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3PD5 · Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UZ14 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase (Q9UZ14) · 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 Q9UZ14
- Elsewhere: RCSB PDB 3PD5 · PDBe 3PD5 · UniProt Q9UZ14
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