Research workbench
Crystal structure of the XI glutathione transferase ECM4 from saccharomyces cerevisiae in complex with glutathione
Analyse Crystal structure of the XI glutathione transferase ECM4 from saccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LKD
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase omega-like 2
- EC
- 2.5.1.18, 1.8.5.1
- UniProt
- P36156
- Ligands
- GSH
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase omega-like 2 (EC 2.5.1.18, 1.8.5.1) | protein | 352 | 45% helix, 7% strand | P36156 |
| B | Glutathione S-transferase omega-like 2 (EC 2.5.1.18, 1.8.5.1) | protein | 338 | 45% helix, 7% strand | P36156 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.74 | 0.92 | 30 | empty |
| 2 | 504 | 0.73 | 0.81 | 52 | GSH |
| 3 | 407 | 0.63 | 0.77 | 41 | GSH |
| 4 | 53 | 0.31 | 0.76 | 14 | empty |
| 5 | 54 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1425 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5LKD · Crystal structure of the Xi glutathione transferase ECM4 from Saccharomyces cerevisiae in… · the same entry in another collection · chain A against A, TM-score 1.00
- P36156 · AlphaFold monomer V2.0 prediction for glutathione S-transferase omega-like 2 (P36156) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P36156
- Elsewhere: RCSB PDB 5LKD · PDBe 5LKD · UniProt P36156
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