MolNFT v1 · #94437 · protein
Crystal structure of E. COLI threonyl-tRNA synthetase bound to a novel inhibitor
4HWR · Threonine--tRNA ligase: “Crystal structure of E. COLI threonyl-tRNA synthetase bound to a novel inhibitor”. X-ray diffraction, 2 ligands (1B2, ZN), 8 pockets (best druggability 0.84). MolNFT v1 #94437 on GenesisL1: 3D structure…
- PDB
- 4HWR
- 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
- P0A8M3
- Ligands
- 1B2, ZN
- Pockets
- 8 · best druggability 0.84
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 | 403 | 38% helix, 27% strand | P0A8M3 |
| B | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 398 | 38% helix, 27% strand | P0A8M3 |
Ligands and binding sites
- 1B2 · N-{[3-(2H-indazol-5-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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.84 | 0.88 | 82 | empty |
| 2 | 489 | 0.71 | 0.81 | 50 | empty |
| 3 | 343 | 0.67 | 0.81 | 41 | ZN, 1B2 |
| 4 | 355 | 0.65 | 0.80 | 39 | ZN, 1B2 |
| 5 | 93 | 0.53 | 0.84 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2181 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 4HWR · 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 A 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 4HWR · PDBe 4HWR · UniProt P0A8M3
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