Research workbench
Glutathione S-transferase omega 1 bound to covalent inhibitor C1-27
Analyse Glutathione S-transferase omega 1 bound to covalent inhibitor C1-27 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YQM
- Type
- protein
- Length
- 711 residues
- Chains
- 3
- 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
- 4G9
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutathione S-transferase omega-1 (EC 2.5.1.18, 1.8.5.1, 1.20.4.2) | protein | 237 | 49% helix, 8% strand | P78417 |
Ligands and binding sites
- 4G9 · 2-chloro-N-[4-chloro-3-(dimethylsulfamoyl)phenyl]acetamide · ligand · 3 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.78 | 0.79 | 96 | 4G9, MES |
| 2 | 317 | 0.61 | 0.78 | 42 | 4G9, MES |
| 3 | 182 | 0.50 | 0.77 | 21 | empty |
| 4 | 158 | 0.45 | 0.75 | 17 | empty |
| 5 | 57 | 0.33 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1030 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4YQM · Glutathione S-transferase Omega 1 bound to covalent inhibitor C1-27 · 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 0.99
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 4YQM · PDBe 4YQM · UniProt P78417
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