MolNFT v1 · #136800 · protein
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem 1917)
5V49 · Methionyl-tRNA synthetase, putative: “Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (chem 1917)”. X-ray diffraction, 2 ligands (MET, 8WA), 14 pockets (best druggability 0.73). MolNFT v1 #136800 on GenesisL1…
- PDB
- 5V49
- Type
- protein
- Length
- 1,050 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionyl-tRNA synthetase, putative
- EC
- 6.1.1.10
- UniProt
- Q38C91
- Ligands
- MET, 8WA
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 517 | 50% helix, 18% strand | Q38C91 |
| B | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 533 | 49% helix, 19% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 8WA · N~1~-(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)-N~2~-[(4R)-6,8-dichloro-1,2,3,4-tetrahydroquinolin-4-yl]-N~1~-methylethane-1,2-diamine · ligand · chains B
- GOL · Glycerol · additive · chains 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 | 465 | 0.73 | 0.82 | 43 | empty |
| 2 | 413 | 0.66 | 0.79 | 48 | 8WA |
| 3 | 354 | 0.60 | 0.76 | 40 | empty |
| 4 | 180 | 0.48 | 0.76 | 25 | empty |
| 5 | 67 | 0.46 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1511 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5V49 · Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 1917) · 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 5V49 · PDBe 5V49 · UniProt Q38C91
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