Research workbench
Structure of human glutathione S-transferase M1A-1A complexed with 1- (S-(glutathionyl)-2,4,6-trinitrocyclohexadienate anion
Analyse Structure of human glutathione S-transferase M1A-1A complexed with 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F3M
- Type
- protein
- Length
- 1,307 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase mu 1
- EC
- 2.5.1.18
- UniProt
- P09488
- Ligands
- GTD
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Glutathione S-transferase mu 1 (EC 2.5.1.18) | protein | 218 | 52% helix, 9% strand | P09488 |
| C | Glutathione S-transferase mu 1 (EC 2.5.1.18) | protein | 217 | 51% helix, 9% strand | P09488 |
Ligands and binding sites
- GTD · 1-(S-glutathionyl)-2,4,6-trinitrocyclohexa-2,5-diene · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.75 | 0.78 | 92 | GTD |
| 2 | 1162 | 0.74 | 0.77 | 81 | GTD |
| 3 | 1199 | 0.74 | 0.77 | 84 | GTD |
| 4 | 181 | 0.62 | 0.83 | 26 | empty |
| 5 | 167 | 0.61 | 0.84 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1397 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1395 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1395 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 386 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2F3M · Structure of human GLUTATHIONE S-TRANSFERASE M1A-1A complexed with… · the same entry in another collection · chain F against F, TM-score 1.00
- P09488 · AlphaFold monomer V2.0 prediction for glutathione S-transferase mu 1 (P09488) · a predicted model of the same protein · chain C 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 P09488
- Elsewhere: RCSB PDB 2F3M · PDBe 2F3M · UniProt P09488
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