MolNFT v1 · #90330 · protein
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor chem 1289
4EG4 · Methionyl-tRNA synthetase, putative: “Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor chem 1289”. X-ray diffraction, 3 ligands (MET, 0OT, SO4), 14 pockets (best druggability 0.80). MolNFT v1 #90330 on…
- PDB
- 4EG4
- Type
- protein
- Length
- 1,033 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, 0OT, SO4
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 522 | 49% helix, 17% strand | Q38C91 |
| B | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 511 | 51% helix, 16% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 0OT · 2-({3-[(3,5-dibromo-2-ethoxybenzyl)amino]propyl}amino)quinolin-4(1H)-one · ligand · chains B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 20 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.80 | 0.84 | 77 | GOL |
| 2 | 473 | 0.68 | 0.79 | 62 | GOL, DMS, MET |
| 3 | 50 | 0.67 | 0.96 | 17 | GOL |
| 4 | 419 | 0.67 | 0.79 | 40 | DMS, SO4, 0OT |
| 5 | 103 | 0.45 | 0.79 | 13 | GOL |
Interfaces
1 interface between chains.
- A–B · 1626 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 4EG4 · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor Chem 1289 · 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 4EG4 · PDBe 4EG4 · UniProt Q38C91
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