Research workbench
ATGSTF2 from arabidopsis thaliana in complex with quercetrin
Analyse ATGSTF2 from arabidopsis thaliana in complex with quercetrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A4W
- Type
- protein
- Length
- 1,258 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase F2
- EC
- 2.5.1.18
- UniProt
- P46422
- Ligands
- QCT
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Glutathione S-transferase F2 (EC 2.5.1.18) | protein | 211 | 57% helix, 9% strand | P46422 |
| B | Glutathione S-transferase F2 (EC 2.5.1.18) | protein | 210 | 57% helix, 9% strand | P46422 |
| F | Glutathione S-transferase F2 (EC 2.5.1.18) | protein | 204 | 59% helix, 9% strand | P46422 |
Ligands and binding sites
- QCT · 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside · ligand · 8 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 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
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.82 | 0.85 | 80 | ACT |
| 2 | 410 | 0.77 | 0.86 | 44 | ACT |
| 3 | 790 | 0.73 | 0.78 | 63 | ACT |
| 4 | 271 | 0.72 | 0.86 | 36 | QCT |
| 5 | 314 | 0.70 | 0.83 | 38 | ACT |
Interfaces
10 interfaces between chains.
- E–F · 1297 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1257 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1235 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 745 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 714 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5A4W · AtGSTF2 from Arabidopsis thaliana in complex with quercetrin · the same entry in another collection · chain F against F, TM-score 1.00
- P46422 · AlphaFold monomer V2.0 prediction for glutathione S-transferase F2 (P46422) · 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 P46422
- Elsewhere: RCSB PDB 5A4W · PDBe 5A4W · UniProt P46422
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