MolNFT v1 · #156857 · protein
Glutathione S-transferase omega 1 bound to covalent inhibitor 37
6MHC · Glutathione S-transferase omega-1: “Glutathione S-transferase omega 1 bound to covalent inhibitor 37”. X-ray diffraction, 1 ligand (JRM), 6 pockets (best druggability 0.79). MolNFT v1 #156857 on GenesisL1: 3D structure, binding…
- PDB
- 6MHC
- Type
- protein
- Length
- 488 residues
- Chains
- 2
- 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
- JRM
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutathione S-transferase omega-1 (EC 2.5.1.18, 1.8.5.1, 1.20.4.2) | protein | 244 | 49% helix, 9% strand | P78417 |
Ligands and binding sites
- JRM · methyl N-(4-phenyl-1,3-thiazol-2-yl)-N-propanoylglycinate · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.79 | 0.80 | 97 | JRM, DMS, MES |
| 2 | 224 | 0.51 | 0.75 | 24 | empty |
| 3 | 177 | 0.47 | 0.75 | 19 | empty |
| 4 | 113 | 0.45 | 0.78 | 19 | empty |
| 5 | 94 | 0.39 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6MHC · Glutathione S-Transferase Omega 1 bound to covalent inhibitor 37 · 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 0.97
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 6MHC · PDBe 6MHC · UniProt P78417
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