MolNFT v1 · #112696 · protein
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (2S)-N-(3,5-dichlorobenzyl)-N'-(1H-IMIDAZO[4,5-B]PYRIDIN-2-yl)-2- methylpropane-1,3-diamine (chem 1655)
4ZT5: “Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor…”. X-ray diffraction, 3 ligands (MET, 4RN, SO4), 13 pockets (best druggability 0.75). MolNFT v1 #112696 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4ZT5
- Type
- protein
- Length
- 1,049 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, 4RN, SO4
- Pockets
- 13 · best druggability 0.75
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 | 521 | 50% helix, 17% strand | Q38C91 |
| B | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 528 | 49% helix, 18% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 4RN · (2S)-N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)-2-methylpropane-1,3-diamine · ligand · chains B
- SO4 · Sulfate ion · ion · chains B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.75 | 0.82 | 52 | empty |
| 2 | 448 | 0.67 | 0.79 | 51 | 4RN |
| 3 | 336 | 0.59 | 0.77 | 32 | DMS |
| 4 | 67 | 0.53 | 0.86 | 26 | MET |
| 5 | 112 | 0.41 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1503 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4ZT5 · 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 4ZT5 · PDBe 4ZT5 · UniProt Q38C91
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