Research workbench
Trypanosoma brucei methionyl-tRNA synthetase in complex with product methionyl-adenylate
Analyse Trypanosoma brucei methionyl-tRNA synthetase in complex with product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EG3
- Type
- protein
- Length
- 1,056 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
- ME8
- Pockets
- 15 · best druggability 0.77
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 | 527 | 48% helix, 18% strand | Q38C91 |
| B | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 529 | 50% helix, 18% strand | Q38C91 |
Ligands and binding sites
- ME8 · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 11 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 | 574 | 0.77 | 0.84 | 61 | empty |
| 2 | 857 | 0.76 | 0.79 | 83 | GOL, ME8 |
| 3 | 813 | 0.76 | 0.80 | 72 | ME8 |
| 4 | 176 | 0.49 | 0.77 | 29 | empty |
| 5 | 135 | 0.44 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1614 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4EG3 · Trypanosoma brucei methionyl-tRNA synthetase in complex with product methionyl-adenylate · 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 4EG3 · PDBe 4EG3 · UniProt Q38C91
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