Research workbench
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor
Analyse Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TQU
- Type
- protein
- Length
- 1,026 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, I53, SO4
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 520 | 50% helix, 17% strand | Q38C91 |
| B | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 506 | 52% helix, 16% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- I53 · 2-[2-[[3-(1~{H}-benzimidazol-2-ylamino) propylamino]methyl]-4,6-bis(chloranyl)indol-1-yl]ethanol · ligand · chains B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.76 | 0.83 | 52 | empty |
| 2 | 388 | 0.65 | 0.79 | 43 | I53, SO4 |
| 3 | 72 | 0.61 | 0.90 | 24 | MET |
| 4 | 345 | 0.59 | 0.76 | 40 | empty |
| 5 | 168 | 0.46 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1490 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5TQU · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor · the same entry in another collection · chain B against B, 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 5TQU · PDBe 5TQU · UniProt Q38C91
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