Research workbench
Structure of homoglutathione synthetase from glycine max in open conformation with gamma-glutamyl-cysteine bound.
Analyse Structure of homoglutathione synthetase from glycine max in open conformation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KAK
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoglutathione synthetase
- EC
- 6.3.2.3
- UniProt
- Q9M426
- Ligands
- 3GC
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoglutathione synthetase (EC 6.3.2.3) | protein | 443 | 40% helix, 27% strand | Q9M426 |
| B | Homoglutathione synthetase (EC 6.3.2.3) | protein | 437 | 40% helix, 26% strand | Q9M426 |
Ligands and binding sites
- 3GC · Gamma-glutamylcysteine · ligand · 3 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 | 867 | 0.73 | 0.78 | 98 | empty |
| 2 | 590 | 0.67 | 0.77 | 63 | 3GC |
| 3 | 388 | 0.61 | 0.77 | 42 | 3GC |
| 4 | 239 | 0.59 | 0.79 | 27 | empty |
| 5 | 99 | 0.57 | 0.86 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1215 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3KAK · Structure of homoglutathione synthetase from Glycine max in open 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 3KAK · PDBe 3KAK · UniProt Q9M426
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