MolNFT v1 · #94435 · protein
Crystal structure of E. COLI threonyl-tRNA synthetase bound to a novel inhibitor
4HWO · Threonine--tRNA ligase: “Crystal structure of E. COLI threonyl-tRNA synthetase bound to a novel inhibitor”. X-ray diffraction, 2 ligands (409, ZN), 7 pockets (best druggability 0.84). MolNFT v1 #94435 on GenesisL1: 3D structure…
- PDB
- 4HWO
- Type
- protein
- Length
- 807 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
- P0A8M3
- Ligands
- 409, ZN
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 409 | 38% helix, 27% strand | P0A8M3 |
| B | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 398 | 40% helix, 28% strand | P0A8M3 |
Ligands and binding sites
- 409 · N-{[3-(4-aminoquinazolin-7-yl)phenyl]sulfonyl}-L-threoninamide · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.84 | 0.95 | 48 | empty |
| 2 | 677 | 0.71 | 0.78 | 62 | empty |
| 3 | 496 | 0.67 | 0.78 | 47 | empty |
| 4 | 356 | 0.66 | 0.80 | 46 | 409 |
| 5 | 320 | 0.64 | 0.80 | 44 | ZN, 409 |
Interfaces
1 interface between chains.
- A–B · 2142 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4HWO · Crystal structure of E. coli Threonyl-tRNA synthetase bound to a novel inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P0A8M3 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase (P0A8M3) · 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 P0A8M3
- Elsewhere: RCSB PDB 4HWO · PDBe 4HWO · UniProt P0A8M3
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