MolNFT v1 · #94439 · protein
Crystal structure of human threonyl-tRNA synthetase bound to a novel inhibitor
4HWT · Threonine--tRNA ligase, cytoplasmic: “Crystal structure of human threonyl-tRNA synthetase bound to a novel inhibitor”. X-ray diffraction, 2 ligands (1B2, ZN), 5 pockets (best druggability 0.82). MolNFT v1 #94439 on GenesisL1: 3D…
- PDB
- 4HWT
- Type
- protein
- Length
- 797 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.3
- UniProt
- P26639
- Ligands
- 1B2, ZN
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine--tRNA ligase, cytoplasmic (EC 6.1.1.3) | protein | 395 | 40% helix, 26% strand | P26639 |
| B | Threonine--tRNA ligase, cytoplasmic (EC 6.1.1.3) | protein | 402 | 40% helix, 25% strand | P26639 |
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
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 | 1112 | 0.82 | 0.83 | 86 | empty |
| 2 | 212 | 0.81 | 0.95 | 34 | empty |
| 3 | 429 | 0.70 | 0.81 | 42 | ZN, 1B2 |
| 4 | 442 | 0.67 | 0.79 | 44 | 1B2 |
| 5 | 146 | 0.49 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2472 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4HWT · Crystal structure of human Threonyl-tRNA synthetase bound to a novel inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P26639 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase 1, cytoplasmic (P26639) · 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 P26639
- Elsewhere: RCSB PDB 4HWT · PDBe 4HWT · UniProt P26639
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