MolNFT v1 · #14175 · protein
Yeast glutathione synthase bound to gamma-glutamyl-cysteine, AMP-pnp and 2 magnesium ions
1M0W · Glutathione synthetase: “Yeast glutathione synthase bound to gamma-glutamyl-cysteine, AMP-pnp and 2 magnesium ions”. X-ray diffraction, 4 ligands (ANP, 3GC, MG), 10 pockets (best druggability 0.76). MolNFT v1 #14175 on GenesisL1: 3D…
- PDB
- 1M0W
- Type
- protein
- Length
- 960 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione synthetase
- EC
- 6.3.2.3
- UniProt
- Q08220
- Ligands
- ANP, 3GC, MG, SO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione synthetase (EC 6.3.2.3) | protein | 481 | 41% helix, 26% strand | Q08220 |
| B | Glutathione synthetase (EC 6.3.2.3) | protein | 479 | 41% helix, 26% strand | Q08220 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- 3GC · Gamma-glutamylcysteine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 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 | 1012 | 0.76 | 0.78 | 90 | MG, ANP, 3GC |
| 2 | 831 | 0.73 | 0.78 | 78 | MG, SO4, ANP, 3GC |
| 3 | 463 | 0.67 | 0.79 | 39 | empty |
| 4 | 444 | 0.67 | 0.79 | 41 | empty |
| 5 | 130 | 0.60 | 0.85 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1843 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1M0W · Yeast Glutathione Synthase Bound to gamma-glutamyl-cysteine, AMP-PNP and 2 Magnesium Ions · the same entry in another collection · chain A against A, TM-score 1.00
- Q08220 · AlphaFold monomer V2.0 prediction for glutathione synthetase (Q08220) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q08220
- Elsewhere: RCSB PDB 1M0W · PDBe 1M0W · UniProt Q08220
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