Research workbench
Trypanosoma brucei methionyl-tRNA synthetase in complex with a quinazolinone inhibitor
Analyse Trypanosoma brucei methionyl-tRNA synthetase in complex with a quinazolinone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NFH
- Type
- protein
- Length
- 1,046 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, 8W2
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 519 | 49% helix, 17% strand | Q38C91 |
| B | Methionyl-tRNA synthetase, putative (EC 6.1.1.10) | protein | 527 | 48% helix, 17% strand | Q38C91 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- 8W2 · 2-[3-[[4,6-bis(chloranyl)-1~{H}-indol-2-yl]methylamino]propylamino]-3~{H}-quinazolin-4-one · ligand · chains B
- GOL · Glycerol · additive · 5 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
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.76 | 0.82 | 61 | empty |
| 2 | 400 | 0.65 | 0.78 | 47 | 8W2 |
| 3 | 352 | 0.61 | 0.77 | 38 | DMS |
| 4 | 124 | 0.55 | 0.82 | 33 | MET |
| 5 | 198 | 0.53 | 0.78 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 1568 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5NFH · Trypanosoma brucei methionyl-tRNA synthetase in complex with a quinazoli 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 5NFH · PDBe 5NFH · UniProt Q38C91
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