Research workbench
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-[(4R)-6,8-dichloro-3,4-dihydro-2H-chromen-4-yl]-N'-(5-fluoro-1H- IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-diamine (chem 1709)
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
- 4ZT6
- Type
- protein
- Length
- 1,054 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, 4RD
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 526 | 50% helix, 18% strand | Q38C91 |
| B | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 528 | 50% helix, 17% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 4RD · N-[(4R)-6,8-dichloro-3,4-dihydro-2H-chromen-4-yl]-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine · ligand · chains B
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.76 | 0.83 | 61 | empty |
| 2 | 772 | 0.75 | 0.79 | 67 | MET, DMS |
| 3 | 412 | 0.66 | 0.78 | 42 | 4RD |
| 4 | 141 | 0.49 | 0.79 | 37 | empty |
| 5 | 130 | 0.40 | 0.75 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1557 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4ZT6 · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor… · 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 4ZT6 · PDBe 4ZT6 · UniProt Q38C91
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