MolNFT v1 · #122960 · protein
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem 1893)
5J59 · Methionyl-tRNA synthetase, putative: “Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem 1893)”. X-ray diffraction, 2 ligands (MET, N93), 13 pockets (best druggability 0.76). MolNFT v1 #122960 on GenesisL1…
- PDB
- 5J59
- Type
- protein
- Length
- 1,050 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, N93
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 517 | 51% helix, 18% strand | Q38C91 |
| B | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 533 | 49% helix, 18% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- N93 · 5-chloro-N-(2-{[(3,5-dichlorophenyl)methyl]amino}ethyl)-N-methyl-3H-imidazo[4,5-b]pyridin-2-amine · ligand · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.76 | 0.82 | 62 | empty |
| 2 | 51 | 0.68 | 0.97 | 16 | empty |
| 3 | 539 | 0.67 | 0.77 | 73 | N93 |
| 4 | 58 | 0.62 | 0.92 | 22 | MET |
| 5 | 360 | 0.61 | 0.77 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 1488 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5J59 · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 1893) · 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 5J59 · PDBe 5J59 · UniProt Q38C91
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