Research workbench
Crystal structure of drosophila melanogaster noppera-bo, glutathione S-transferase epsilon 14 (DMGSTE14), in TDP011-bound form
Analyse Crystal structure of drosophila melanogaster noppera-bo, glutathione… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DB3
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase E14
- EC
- 2.5.1.18
- UniProt
- Q7JYX0
- Ligands
- H2X, GSH
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase E14 (EC 2.5.1.18) | protein | 223 | 61% helix, 8% strand | Q7JYX0 |
| B | Glutathione S-transferase E14 (EC 2.5.1.18) | protein | 218 | 61% helix, 8% strand | Q7JYX0 |
Ligands and binding sites
- H2X · 4-bromanyl-2-[[2-[(E)-1-(3-methoxyphenyl) ethylideneamino]propan-2-ylamino]methyl]phenol · ligand · 2 copies · chains A, B
- GSH · Glutathione · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.80 | 0.82 | 77 | H2X, GSH |
| 2 | 100 | 0.38 | 0.76 | 23 | empty |
| 3 | 104 | 0.38 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1436 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7DB3 · Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7JYX0 · AlphaFold monomer V2.0 prediction for glutathione S-transferase E14 (Q7JYX0) · a predicted model of the same protein · chain B 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 Q7JYX0
- Elsewhere: RCSB PDB 7DB3 · PDBe 7DB3 · UniProt Q7JYX0
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