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Crystal structure of lolium rigidum gstf in complex with S-(P- nitrobenzyl) glutathione
Analyse Crystal structure of lolium rigidum gstf in complex with S-(P- nitrobenzyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZB6
- Type
- protein
- Length
- 1,309 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione transferase
- UniProt
- M5BPX4
- Ligands
- GTB, GSH, NA
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione transferase | protein | 222 | 59% helix, 8% strand | M5BPX4 |
| C | Glutathione transferase | protein | 227 | 56% helix, 9% strand | M5BPX4 |
| E, B, F, D | Glutathione transferase | protein | 215 | 58% helix, 8% strand | M5BPX4 |
Ligands and binding sites
- GTB · S-(P-nitrobenzyl)glutathione · ligand · 5 copies · chains A, E, C, F, B
- GSH · Glutathione · ligand · chains D
- NA · Sodium ion · metal · 9 copies · chains A, E, C, B, F, D
- GOL · Glycerol · additive · 10 copies · chains A, E, C, F, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.73 | 0.77 | 80 | GTB, GOL, NA |
| 2 | 803 | 0.70 | 0.76 | 72 | GTB, GOL |
| 3 | 54 | 0.69 | 0.97 | 25 | empty |
| 4 | 261 | 0.61 | 0.80 | 43 | empty |
| 5 | 286 | 0.59 | 0.78 | 29 | GTB, GOL |
Interfaces
5 interfaces between chains.
- A–E · 1484 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 1465 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 644 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 538 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6ZB6 · Crystal structure of Lolium rigidum GSTF in complex with S-(p-nitrobenzyl) glutathione · the same entry in another collection · chain A against A, 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 M5BPX4
- Elsewhere: RCSB PDB 6ZB6 · PDBe 6ZB6 · UniProt M5BPX4
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