Research workbench
Crystal structure of glutathione transferase F5 from populus trichocarpa
Analyse Crystal structure of glutathione transferase F5 from populus trichocarpa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F05
- Type
- protein
- Length
- 842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phi class glutathione transferase GSTF5
- UniProt
- D2WL63
- Ligands
- GSH, MG
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phi class glutathione transferase GSTF5 | protein | 210 | 58% helix, 9% strand | D2WL63 |
| C, D | Phi class glutathione transferase GSTF5 | protein | 211 | 59% helix, 9% strand | D2WL63 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- 12P · Dodecaethylene glycol · additive · 2 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.70 | 0.76 | 68 | GSH |
| 2 | 697 | 0.68 | 0.76 | 76 | GSH |
| 3 | 236 | 0.61 | 0.80 | 30 | 12P |
| 4 | 193 | 0.59 | 0.81 | 30 | 12P |
| 5 | 296 | 0.53 | 0.74 | 29 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1384 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1380 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 158 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5F05 · Crystal structure of glutathione transferase F5 from Populus trichocarpa · the same entry in another collection · chain B against B, TM-score 1.00
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 D2WL63
- Elsewhere: RCSB PDB 5F05 · PDBe 5F05 · UniProt D2WL63
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