MolNFT v1 · #77796 · protein
Crystal structure of human kappa class glutathione transferase in complex with S-hexylglutathione
3RPN · Glutathione S-transferase kappa 1: “Crystal structure of human kappa class glutathione transferase in complex with S-hexylglutathione”. X-ray diffraction, 1 ligand (GTX), 12 pockets (best druggability 0.87). MolNFT v1 #77796 on…
- PDB
- 3RPN
- Type
- protein
- Length
- 1,320 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase kappa 1
- EC
- 2.5.1.18
- UniProt
- Q9Y2Q3
- Ligands
- GTX
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutathione S-transferase kappa 1 (EC 2.5.1.18) | protein | 220 | 55% helix, 12% strand | Q9Y2Q3 |
Ligands and binding sites
- GTX · S-hexylglutathione · ligand · 6 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.87 | 0.87 | 80 | GTX |
| 2 | 1056 | 0.86 | 0.87 | 98 | GTX |
| 3 | 928 | 0.86 | 0.87 | 81 | GTX |
| 4 | 1185 | 0.83 | 0.84 | 103 | empty |
| 5 | 1112 | 0.83 | 0.84 | 98 | empty |
Interfaces
11 interfaces between chains.
- B–E · 1446 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1432 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 1410 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 489 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 486 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3RPN · Crystal structure of human kappa class glutathione transferase in complex with… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9Y2Q3 · AlphaFold monomer V2.0 prediction for glutathione S-transferase kappa 1 (Q9Y2Q3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9Y2Q3
- Elsewhere: RCSB PDB 3RPN · PDBe 3RPN · UniProt Q9Y2Q3
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