MolNFT v1 · #122961 · protein
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem 70786556)
5J5A · Methionyl-tRNA synthetase, putative: “Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem 70786556)”. X-ray diffraction, 2 ligands (MET, 756), 16 pockets (best druggability 0.75). MolNFT v1 #122961 on…
- PDB
- 5J5A
- Type
- protein
- Length
- 1,041 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionyl-tRNA synthetase, putative
- EC
- 6.1.1.10
- UniProt
- Q38C91
- Ligands
- MET, 756
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 518 | 50% helix, 18% strand | Q38C91 |
| B | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 523 | 49% helix, 17% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 756 · [(3S)-3-(1H-benzimidazol-2-yl)piperidin-1-yl](2-methyl-1-benzofuran-5-yl)methanone · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.75 | 0.83 | 52 | empty |
| 2 | 401 | 0.65 | 0.78 | 50 | 756 |
| 3 | 74 | 0.63 | 0.91 | 25 | MET |
| 4 | 331 | 0.59 | 0.77 | 34 | empty |
| 5 | 146 | 0.50 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1542 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5J5A · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 70786556) · 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 Q38C91
- Elsewhere: RCSB PDB 5J5A · PDBe 5J5A · UniProt Q38C91
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.