Research workbench
Threonyl-tRNA synthetase from salmonella enterica in complex with an inhibitor
Analyse Threonyl-tRNA synthetase from salmonella enterica in complex with an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L2Q
- Type
- protein
- Length
- 802 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine--tRNA ligase
- EC
- 6.1.1.3
- UniProt
- V7II86
- Ligands
- E4O, ZN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 402 | 38% helix, 28% strand | V7II86 |
| B | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 400 | 38% helix, 27% strand | V7II86 |
Ligands and binding sites
- E4O · (2S,3R)-2-azanyl-N-[(E)-4-[6,7-bis(chloranyl)-4-oxidanylidene-quinazolin-3-yl]but-2-enyl]-3-oxidanyl-butanamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.83 | 0.94 | 47 | empty |
| 2 | 974 | 0.75 | 0.78 | 100 | empty |
| 3 | 433 | 0.67 | 0.79 | 38 | E4O |
| 4 | 437 | 0.65 | 0.78 | 46 | ZN, E4O |
| 5 | 50 | 0.26 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2189 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6L2Q · Threonyl-tRNA synthetase from Salmonella enterica in complex with an inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 V7II86
- Elsewhere: RCSB PDB 6L2Q · PDBe 6L2Q · UniProt V7II86
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