Research workbench
Crystal structure of mu class glutathione S-transferase (GSTM2-2) in complex with glutathione and 6-(7-nitro-2,1,3-benzoxadiazol-4- YLTHIO)HEXANOL (nbdhex)
Analyse Crystal structure of mu class glutathione S-transferase (GSTM2-2) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GUR
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase mu 2
- EC
- 2.5.1.18
- UniProt
- P28161
- Ligands
- BYG, GSH
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glutathione S-transferase mu 2 (EC 2.5.1.18) | protein | 217 | 51% helix, 10% strand | P28161 |
| B | Glutathione S-transferase mu 2 (EC 2.5.1.18) | protein | 216 | 51% helix, 10% strand | P28161 |
Ligands and binding sites
- BYG · L-gamma-glutamyl-S-{(4R)-4-[(6-hydroxyhexyl)sulfanyl]-7-nitro-4,5-dihydro-2,1,3-benzoxadiazol-4-yl}-L-cysteinylglycine · ligand · 2 copies · chains A, B, C, D
- GSH · Glutathione · ligand · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.77 | 0.79 | 88 | BYG, GSH |
| 2 | 924 | 0.76 | 0.79 | 83 | BYG, GSH |
| 3 | 332 | 0.55 | 0.75 | 37 | empty |
| 4 | 123 | 0.45 | 0.78 | 23 | empty |
| 5 | 96 | 0.43 | 0.79 | 22 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1446 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1420 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 93 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3GUR · Crystal Structure of mu class glutathione S-transferase (GSTM2-2) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P28161 · AlphaFold monomer V2.0 prediction for glutathione S-transferase mu 2 (P28161) · 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 P28161
- Elsewhere: RCSB PDB 3GUR · PDBe 3GUR · UniProt P28161
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