MolNFT v1 · #100400 · protein
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-thiophen-3-ylurea (chem 1433) and ATP analog amppcp
4MWD: “Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor…”. X-ray diffraction, 4 ligands (MET, 43E, ACP), 11 pockets (best druggability 0.77). MolNFT v1 #100400 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4MWD
- 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, 43E, ACP, SO4
- Pockets
- 11 · 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 (EC 6.1.1.10) | protein | 531 | 50% helix, 18% strand | Q38C91 |
| B | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 533 | 49% helix, 18% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 43E · 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.77 | 0.83 | 64 | empty |
| 2 | 830 | 0.76 | 0.80 | 76 | DMS, MET |
| 3 | 678 | 0.70 | 0.77 | 76 | GOL, 43E, ACP |
| 4 | 121 | 0.41 | 0.76 | 28 | empty |
| 5 | 116 | 0.41 | 0.76 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1473 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 4MWD · 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 4MWD · PDBe 4MWD · UniProt Q38C91
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