Research workbench
Crystal structure solution of rice GST1 (OSGSTU1) in complex with glutathione.
Analyse Crystal structure solution of rice GST1 (OSGSTU1) in complex with glutathione. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OYJ
- Type
- protein
- Length
- 902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase
- EC
- 2.5.1.18
- UniProt
- O65032
- Ligands
- GSH, MG, CL
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase (EC 2.5.1.18) | protein | 228 | 60% helix, 7% strand | O65032 |
| B | Glutathione S-transferase (EC 2.5.1.18) | protein | 224 | 58% helix, 8% strand | O65032 |
| C | Glutathione S-transferase (EC 2.5.1.18) | protein | 227 | 59% helix, 7% strand | O65032 |
| D | Glutathione S-transferase (EC 2.5.1.18) | protein | 223 | 56% helix, 9% strand | O65032 |
Ligands and binding sites
- GSH · Glutathione · ligand · 7 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, C
- CL · Chloride ion · ion · 20 copies · chains B, D, C, A
- GOL · Glycerol · additive · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.78 | 0.82 | 72 | GSH |
| 2 | 522 | 0.73 | 0.82 | 50 | GSH |
| 3 | 448 | 0.62 | 0.76 | 48 | CL |
| 4 | 184 | 0.57 | 0.81 | 33 | empty |
| 5 | 165 | 0.55 | 0.81 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1376 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1328 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 207 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1OYJ · Crystal structure solution of Rice GST1 (OsGSTU1) in complex with glutathione. · 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 O65032
- Elsewhere: RCSB PDB 1OYJ · PDBe 1OYJ · UniProt O65032
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