Research workbench
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitorn-(3,5-dichlorobenzyl)-2,2-difluoro-N'-(1H-IMIDAZO[4,5- B]PYRIDIN-2-YL)PROPANE-1,3-diamine (chem 1708)
Analyse Trypanosoma brucei methionyl-tRNA synthetase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZT4
- Type
- protein
- Length
- 1,048 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, 4RO, SO4
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 523 | 50% helix, 17% strand | Q38C91 |
| B | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 525 | 49% helix, 17% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 4RO · N-(3,5-dichlorobenzyl)-2,2-difluoro-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine · ligand · chains B
- SO4 · Sulfate ion · ion · chains B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
- GOL · Glycerol · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.75 | 0.83 | 53 | empty |
| 2 | 50 | 0.70 | 0.98 | 16 | empty |
| 3 | 452 | 0.69 | 0.80 | 57 | MET, DMS |
| 4 | 427 | 0.66 | 0.79 | 51 | 4RO |
| 5 | 96 | 0.57 | 0.85 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1529 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4ZT4 · Trypanosoma brucei methionyl-tRNA synthetase in complex with… · 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 4ZT4 · PDBe 4ZT4 · UniProt Q38C91
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