Research workbench
Human glutathione transferase OMEGA1 covalently bound to ML175 inhibitor
Analyse Human glutathione transferase OMEGA1 covalently bound to ML175 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YVO
- Type
- protein
- Length
- 239 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase omega-1
- EC
- 2.5.1.18, 1.8.5.1, 1.20.4.2
- UniProt
- P78417
- Ligands
- MLX, SO4
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase omega-1 (EC 2.5.1.18, 1.8.5.1, 1.20.4.2) | protein | 239 | 54% helix, 9% strand | P78417 |
Ligands and binding sites
- MLX · N-{3-[(2-chloro-acetyl)-(4-nitro-phenyl)-amino]-propyl}-2,2,2-trifluoro-acetamide · ligand · 2 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.59 | 0.79 | 29 | MLX |
| 2 | 71 | 0.29 | 0.73 | 17 | SO4 |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5YVO · Human Glutathione Transferase Omega1 covalently bound to ML175 inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P78417 · AlphaFold monomer V2.0 prediction for glutathione S-transferase omega-1 (P78417) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P78417
- Elsewhere: RCSB PDB 5YVO · PDBe 5YVO · UniProt P78417
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