MolNFT v1 · #122959 · protein
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem 1856)
5J58 · Methionyl-tRNA synthetase, putative: “Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem 1856)”. X-ray diffraction, 2 ligands (MET, N56), 15 pockets (best druggability 0.76). MolNFT v1 #122959 on GenesisL1…
- PDB
- 5J58
- 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, N56
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 519 | 50% helix, 18% strand | Q38C91 |
| B | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 531 | 49% helix, 18% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- N56 · (3S)-1-(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)-N-[(3,5-dichlorophenyl)methyl]piperidin-3-amine · ligand · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.76 | 0.84 | 53 | empty |
| 2 | 442 | 0.67 | 0.79 | 59 | MET, DMS |
| 3 | 482 | 0.67 | 0.78 | 50 | N56 |
| 4 | 107 | 0.43 | 0.77 | 13 | empty |
| 5 | 118 | 0.41 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1557 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5J58 · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 1856) · 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 5J58 · PDBe 5J58 · UniProt Q38C91
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