Research workbench
Structure of homoglutathione synthetase from glycine max in closed conformation with homoglutathione, ADP, a sulfate ion, and three magnesium ions bound
Analyse Structure of homoglutathione synthetase from glycine max in closed conformation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KAL
- Type
- protein
- Length
- 938 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoglutathione synthetase
- EC
- 6.3.2.23
- UniProt
- Q9M426
- Ligands
- HGS, ADP, MG, SO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoglutathione synthetase (EC 6.3.2.23) | protein | 470 | 41% helix, 26% strand | Q9M426 |
| B | Homoglutathione synthetase (EC 6.3.2.23) | protein | 468 | 41% helix, 25% strand | Q9M426 |
Ligands and binding sites
- HGS · D-gamma-glutamyl-L-cysteinyl-beta-alanine · ligand · 4 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.81 | 0.87 | 63 | ADP, HGS, MG, SO4 |
| 2 | 544 | 0.80 | 0.86 | 58 | ADP, HGS, MG, SO4 |
| 3 | 541 | 0.70 | 0.79 | 49 | empty |
| 4 | 489 | 0.68 | 0.79 | 50 | empty |
| 5 | 203 | 0.64 | 0.84 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1294 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3KAL · Structure of homoglutathione synthetase from Glycine max in closed conformation with… · 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 Q9M426
- Elsewhere: RCSB PDB 3KAL · PDBe 3KAL · UniProt Q9M426
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