MolNFT v1 · #125818 · protein
Crystal structure of the XI glutathione transferase ECM4 from saccharomyces cerevisiae in complex with glutathione
5LKD · Glutathione S-transferase omega-like 2: “Crystal structure of the XI glutathione transferase ECM4 from saccharomyces cerevisiae in complex with…”. X-ray diffraction, 1 ligand (GSH), 5 pockets (best druggability 0.74). MolNFT v1…
- 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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