Research workbench
Crystal structure of a bacterial glutathione transferase
Analyse Crystal structure of a bacterial glutathione transferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GDR
- Type
- protein
- Length
- 1,209 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase
- EC
- 2.5.1.18
- Ligands
- GSH
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Glutathione S-transferase (EC 2.5.1.18) | protein | 202 | 51% helix, 10% strand | — |
| B, D, F | Glutathione S-transferase (EC 2.5.1.18) | protein | 201 | 52% helix, 10% strand | — |
Ligands and binding sites
- GSH · Glutathione · ligand · 9 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.75 | 0.81 | 52 | empty |
| 2 | 878 | 0.75 | 0.78 | 79 | GSH |
| 3 | 888 | 0.75 | 0.78 | 74 | GSH |
| 4 | 879 | 0.74 | 0.78 | 73 | GSH |
| 5 | 275 | 0.57 | 0.77 | 36 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1612 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1598 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1582 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 542 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 309 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GDR · Crystal structure of a bacterial glutathione transferase · 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
- Elsewhere: RCSB PDB 2GDR · PDBe 2GDR
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