MolNFT v1 · #100399 · protein
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[(2-methyl-1-benzothiophen-3-YL)METHYL]AMINO}PROPYL)-3- thiophen-3-ylurea (chem 1540)
4MWC: “Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor…”. X-ray diffraction, 3 ligands (MET, 2EM, SO4), 13 pockets (best druggability 0.76). MolNFT v1 #100399 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4MWC
- Type
- protein
- Length
- 1,064 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, 2EM, SO4
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 531 | 49% helix, 18% strand | Q38C91 |
| B | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 533 | 48% helix, 18% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 2EM · 1-(3-{[(2-methyl-1-benzothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea · ligand · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.76 | 0.80 | 70 | DMS, MET |
| 2 | 516 | 0.75 | 0.83 | 53 | empty |
| 3 | 635 | 0.70 | 0.78 | 73 | DMS, 2EM |
| 4 | 69 | 0.47 | 0.83 | 15 | empty |
| 5 | 157 | 0.46 | 0.76 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1501 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4MWC · 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 4MWC · PDBe 4MWC · UniProt Q38C91
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