Research workbench
Editing domain of threonyl-tRNA synthetase from methanococcus jannaschii with L-SER3AA
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
- 4RRF
- Type
- protein
- Length
- 833 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine--tRNA ligase
- EC
- 6.1.1.3
- UniProt
- Q58597
- Ligands
- A3S, MG, CL
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 138 | 32% helix, 41% strand | Q58597 |
| B | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 137 | 32% helix, 41% strand | Q58597 |
| C, D | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 139 | 32% helix, 40% strand | Q58597 |
| E, F | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 140 | 32% helix, 40% strand | Q58597 |
Ligands and binding sites
- A3S · Serine-3'-aminoadenosine · ligand · 6 copies · chains A, D, B, C, E, F
- MG · Magnesium ion · metal · 2 copies · chains B, C, D
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.77 | 0.99 | 14 | empty |
| 2 | 61 | 0.74 | 0.97 | 14 | empty |
| 3 | 157 | 0.73 | 0.90 | 30 | empty |
| 4 | 240 | 0.64 | 0.82 | 25 | A3S |
| 5 | 211 | 0.63 | 0.83 | 27 | A3S |
Interfaces
5 interfaces between chains.
- A–D · 1045 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1010 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1009 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 336 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 256 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4RRF · Editing domain of threonyl-tRNA synthetase from Methanococcus jannaschii with L-Ser3AA · 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 4RRF · PDBe 4RRF · UniProt Q58597
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.