Research workbench
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor chem 1325
Analyse Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor chem 1325 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EG6
- Type
- protein
- Length
- 1,041 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, 0P5, SO4
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 526 | 50% helix, 17% strand | Q38C91 |
| B | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 515 | 50% helix, 15% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 0P5 · 4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(2-chloro-4-methoxyphenoxy)pyrimidin-2-yl}piperazin-2-one · ligand · chains B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 15 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.74 | 0.82 | 52 | GOL |
| 2 | 50 | 0.68 | 0.97 | 18 | GOL |
| 3 | 533 | 0.67 | 0.77 | 55 | 0P5, GOL |
| 4 | 120 | 0.65 | 0.88 | 17 | empty |
| 5 | 319 | 0.61 | 0.78 | 35 | DMS |
Interfaces
1 interface between chains.
- A–B · 1556 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4EG6 · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor Chem 1325 · 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 4EG6 · PDBe 4EG6 · UniProt Q38C91
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