Research workbench
Crystal structure of the theta class glutathione S-transferase from the citrus canker pathogen xanthomonas axonopodis pv. citri with glutathione bound
Analyse Crystal structure of the theta class glutathione S-transferase from the citrus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NV6
- Type
- protein
- Length
- 778 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase
- EC
- 2.5.1.18
- UniProt
- Q8PG02
- Ligands
- GSH, CL
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase (EC 2.5.1.18) | protein | 189 | 61% helix, 9% strand | Q8PG02 |
| B | Glutathione S-transferase (EC 2.5.1.18) | protein | 207 | 60% helix, 9% strand | Q8PG02 |
| C | Glutathione S-transferase (EC 2.5.1.18) | protein | 192 | 60% helix, 8% strand | Q8PG02 |
| D | Glutathione S-transferase (EC 2.5.1.18) | protein | 190 | 61% helix, 9% strand | Q8PG02 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.70 | 0.80 | 57 | CL |
| 2 | 361 | 0.64 | 0.79 | 35 | GSH, CL |
| 3 | 175 | 0.54 | 0.79 | 28 | CL |
| 4 | 192 | 0.51 | 0.78 | 32 | CL |
| 5 | 100 | 0.48 | 0.81 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1145 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1104 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 361 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 155 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6NV6 · Crystal structure of the theta class glutathione S-transferase from the citrus canker… · 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 Q8PG02
- Elsewhere: RCSB PDB 6NV6 · PDBe 6NV6 · UniProt Q8PG02
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