Research workbench
Crystal structure of delta-class glutathione transferase from silkmoth
Analyse Crystal structure of delta-class glutathione transferase from silkmoth in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VK9
- Type
- protein
- Length
- 857 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase delta
- EC
- 2.5.1.18
- UniProt
- Q60GK5
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase delta (EC 2.5.1.18) | protein | 214 | 63% helix, 8% strand | Q60GK5 |
| B | Glutathione S-transferase delta (EC 2.5.1.18) | protein | 213 | 63% helix, 7% strand | Q60GK5 |
| C, D | Glutathione S-transferase delta (EC 2.5.1.18) | protein | 215 | 64% helix, 8% strand | Q60GK5 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.79 | 0.81 | 78 | empty |
| 2 | 781 | 0.76 | 0.80 | 54 | empty |
| 3 | 438 | 0.68 | 0.80 | 37 | empty |
| 4 | 87 | 0.44 | 0.80 | 19 | empty |
| 5 | 74 | 0.37 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1536 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 720 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 691 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VK9 · Crystal structure of delta-class glutathione transferase from silkmoth · the same entry in another collection · chain C against C, 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 Q60GK5
- Elsewhere: RCSB PDB 3VK9 · PDBe 3VK9 · UniProt Q60GK5
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