Research workbench
Crystal structure of the editing domain of threonyl-tRNA synthetase from pyrococcus abyssi in complex with glycyl-3'-aminoadenosine
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
- 3PD4
- 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
- A3G
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 146 | 31% helix, 38% strand | Q9UZ14 |
| B | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 143 | 34% helix, 39% strand | Q9UZ14 |
Ligands and binding sites
- A3G · 3'-deoxy-3'-(glycylamino)adenosine · ligand · 2 copies · 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 | 58 | 0.76 | 0.99 | 14 | empty |
| 2 | 200 | 0.64 | 0.84 | 29 | A3G |
| 3 | 180 | 0.64 | 0.84 | 30 | A3G |
| 4 | 72 | 0.34 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1157 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3PD4 · Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UZ14 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase (Q9UZ14) · a predicted model of the same protein · chain B 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 3PD4 · PDBe 3PD4 · UniProt Q9UZ14
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