MolNFT v1 · #113087 · protein
ATGSTF2 from arabidopsis thaliana in complex with indole-3-aldehyde
5A4U · Glutathione S-transferase F2: “ATGSTF2 from arabidopsis thaliana in complex with indole-3-aldehyde”. X-ray diffraction, 1 ligand (I3A), 18 pockets (best druggability 0.81). MolNFT v1 #113087 on GenesisL1: 3D structure, binding sites…
- PDB
- 5A4U
- Type
- protein
- Length
- 1,260 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
- I3A
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 59% 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 | 59% helix, 9% strand | P46422 |
| B | Glutathione S-transferase F2 (EC 2.5.1.18) | protein | 210 | 58% helix, 9% strand | P46422 |
| F | Glutathione S-transferase F2 (EC 2.5.1.18) | protein | 206 | 60% helix, 9% strand | P46422 |
Ligands and binding sites
- I3A · 1H-indole-3-carbaldehyde · ligand · 8 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.81 | 0.85 | 74 | ACT |
| 2 | 349 | 0.76 | 0.86 | 41 | ACT |
| 3 | 78 | 0.73 | 0.97 | 16 | empty |
| 4 | 651 | 0.73 | 0.80 | 66 | empty |
| 5 | 265 | 0.71 | 0.86 | 37 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1312 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1307 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1234 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 724 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 675 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5A4U · AtGSTF2 from Arabidopsis thaliana in complex with indole-3-aldehyde · 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 5A4U · PDBe 5A4U · UniProt P46422
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