Research workbench
Structure of IDP01693/YJEA, a potential T-RNA synthetase from salmonella typhimurium
Analyse Structure of IDP01693/YJEA, a potential T-RNA synthetase from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G1Z
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative lysyl-tRNA synthetase
- EC
- 6.1.1.6
- UniProt
- Q9ZJ12
- Ligands
- AMP, PO4, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative lysyl-tRNA synthetase (EC 6.1.1.6) | protein | 317 | 40% helix, 21% strand | Q9ZJ12 |
| B | Putative lysyl-tRNA synthetase (EC 6.1.1.6) | protein | 309 | 38% helix, 22% strand | Q9ZJ12 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · chains 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 | 114 | 0.76 | 0.96 | 22 | empty |
| 2 | 621 | 0.74 | 0.81 | 62 | AMP, PO4 |
| 3 | 640 | 0.73 | 0.80 | 60 | AMP, PO4 |
| 4 | 161 | 0.48 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2430 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 3G1Z · Structure of IDP01693/yjeA, a potential t-RNA synthetase from Salmonella typhimurium · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZJ12 · AlphaFold monomer V2.0 prediction for elongation factor P--(R)-beta- lysine ligase… · 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 Q9ZJ12
- Elsewhere: RCSB PDB 3G1Z · PDBe 3G1Z · UniProt Q9ZJ12
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