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Crystal structure of threonyl-tRNA synthetase (thrrs) from salmonella enterica in complex with an inhibitor
Analyse Crystal structure of threonyl-tRNA synthetase (thrrs) from salmonella enterica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CBG
- Type
- protein
- Length
- 801 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
- FQL, ZN
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 401 | 37% helix, 27% strand | V7II86 |
| B | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 400 | 38% helix, 27% strand | V7II86 |
Ligands and binding sites
- FQL · (2S,3R)-N-[(E)-4-[6,7-bis(chloranyl)-4-oxidanylidene-quinazolin-3-yl]but-2-enyl]-2-(methylamino)-3-oxidanyl-butanamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.84 | 0.95 | 47 | empty |
| 2 | 961 | 0.75 | 0.78 | 101 | empty |
| 3 | 460 | 0.68 | 0.79 | 39 | FQL, ZN |
| 4 | 450 | 0.66 | 0.79 | 45 | FQL, ZN |
| 5 | 86 | 0.34 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2190 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 7CBG · Crystal structure of threonyl-tRNA synthetase (ThrRS) from Salmonella enterica in complex… · 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 7CBG · PDBe 7CBG · UniProt V7II86
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