Research workbench
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem 1907)
Analyse Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MES
- Type
- protein
- Length
- 1,052 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionyl-tRNA synthetase
- EC
- 6.1.1.10
- UniProt
- Q38C91
- Ligands
- MET, JFA
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 521 | 50% helix, 17% strand | Q38C91 |
| B | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 531 | 48% helix, 18% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- JFA · 1-[(1H-benzimidazol-2-yl)methyl]-4-[(2,4-dichlorophenyl)methyl]-1,3-dihydro-2H-imidazol-2-one · ligand · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.75 | 0.83 | 52 | empty |
| 2 | 452 | 0.66 | 0.78 | 52 | JFA |
| 3 | 372 | 0.62 | 0.77 | 36 | empty |
| 4 | 64 | 0.58 | 0.90 | 24 | MET |
| 5 | 167 | 0.48 | 0.76 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1596 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6MES · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 1907) · 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 6MES · PDBe 6MES · UniProt Q38C91
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