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Editing domain of threonyl-tRNA synthetase from Methanococcus jannaschii with L-Thr3AA
Analyse Editing domain of threonyl-tRNA synthetase from Methanococcus jannaschii with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RRG
- Type
- protein
- Length
- 551 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.93
- Source
- Methanocaldococcus jannaschii
- Molecule
- Threonine--tRNA ligase
- EC
- 6.1.1.3
- UniProt
- Q58597
- Ligands
- A3T
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.93 · 2 distinct chains · 32% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 138 | 31% helix, 41% strand | Q58597 |
| C | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 137 | 32% helix, 41% strand | Q58597 |
Ligands and binding sites
- A3T · 3'-deoxy-3'-(L-threonylamino)adenosine · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.77 | 0.99 | 14 | empty |
| 2 | 239 | 0.64 | 0.82 | 27 | A3T |
| 3 | 225 | 0.63 | 0.82 | 26 | A3T |
| 4 | 271 | 0.61 | 0.80 | 30 | empty |
| 5 | 240 | 0.61 | 0.80 | 29 | A3T |
Interfaces
3 interfaces between chains.
- C–D · 1158 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1104 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 177 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4RRG · Editing domain of threonyl-tRNA synthetase from methanococcus jannaschii with L-THR3AA · the same entry in another collection · chain D against D, TM-score 1.00
- Q58597 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase (Q58597) · 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 Q58597
- Elsewhere: RCSB PDB 4RRG · PDBe 4RRG · UniProt Q58597
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