Research workbench
Camel GSTM1-1 in complex with S-(P-NITROBENZYL)GLUTATHIONE
Analyse Camel GSTM1-1 in complex with S-(P-NITROBENZYL)GLUTATHIONE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OPY
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione transferase
- EC
- 2.5.1.18
- UniProt
- G9B5E4
- Ligands
- GTB, NA
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, A, B, C | Glutathione transferase (EC 2.5.1.18) | protein | 217 | 51% helix, 9% strand | G9B5E4 |
Ligands and binding sites
- GTB · S-(P-nitrobenzyl)glutathione · ligand · 4 copies · chains F, B, A, C
- NA · Sodium ion · metal · 4 copies · chains F, A, C, B
- FMT · Formic acid · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.75 | 0.77 | 84 | GTB |
| 2 | 1038 | 0.74 | 0.77 | 80 | GTB, FMT |
| 3 | 643 | 0.70 | 0.78 | 59 | empty |
| 4 | 135 | 0.55 | 0.82 | 18 | empty |
| 5 | 51 | 0.36 | 0.80 | 16 | empty |
Interfaces
5 interfaces between chains.
- F–B · 1457 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1456 Ų buried · 24 hydrogen bonds · protein-protein
- F–C · 232 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
- F–A · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 7OPY · Camel GSTM1-1 in complex with S-(p-nitrobenzyl)glutathione · the same entry in another collection · chain F against F, 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 G9B5E4
- Elsewhere: RCSB PDB 7OPY · PDBe 7OPY · UniProt G9B5E4
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