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
- 7WM7
- 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
- 9I6, ZN
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 401 | 38% helix, 30% strand | V7II86 |
| B | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 400 | 37% helix, 28% strand | V7II86 |
Ligands and binding sites
- 9I6 · (2S,3R)-2-azanyl-N-[5-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)pentyl]-3-oxidanyl-N-[[3-(1-oxidanylidene-2,3-dihydroisoindol-5-yl) phenyl]methyl]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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.80 | 0.82 | 125 | empty |
| 2 | 457 | 0.68 | 0.79 | 40 | ZN, 9I6 |
| 3 | 408 | 0.67 | 0.80 | 38 | ZN, 9I6 |
| 4 | 87 | 0.33 | 0.74 | 22 | empty |
| 5 | 60 | 0.27 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2163 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 7WM7 · 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 7WM7 · PDBe 7WM7 · UniProt V7II86
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