MolNFT v1 · #100385 · protein
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-(3-HYDROXYPHENYL)UREA (chem 1387)
4MVY: “Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor…”. X-ray diffraction, 2 ligands (MET, 387), 12 pockets (best druggability 0.77). MolNFT v1 #100385 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MVY
- Type
- protein
- Length
- 1,061 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, 387
- Pockets
- 12 · 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 | 530 | 49% helix, 17% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 387 · 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(3-hydroxyphenyl)urea · ligand · chains B
- GOL · Glycerol · additive · 8 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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.77 | 0.82 | 59 | empty |
| 2 | 927 | 0.75 | 0.78 | 88 | DMS, MET |
| 3 | 500 | 0.69 | 0.79 | 52 | 387 |
| 4 | 167 | 0.50 | 0.78 | 35 | empty |
| 5 | 163 | 0.44 | 0.75 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1509 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4MVY · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor… · the same entry in another collection · chain B against B, 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 4MVY · PDBe 4MVY · UniProt Q38C91
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