Research workbench
E. COLI bifunctional glutathionylspermidine SYNTHETASE/AMIDASE incomplex with MG2+ and ADP and phosphinate inhibitor
Analyse E. COLI bifunctional glutathionylspermidine SYNTHETASE/AMIDASE incomplex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IOA
- Type
- protein
- Length
- 1,178 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional glutathionylspermidine SYNTHETASE/AMIDASE
- EC
- 6.3.1.8, 3.5.1.78
- UniProt
- P0AES0
- Ligands
- GGA, ADP, MG
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional glutathionylspermidine SYNTHETASE/AMIDASE (EC 6.3.1.8, 3.5.1.78) | protein | 589 | 27% helix, 28% strand | P0AES0 |
| B | Bifunctional glutathionylspermidine SYNTHETASE/AMIDASE (EC 6.3.1.8, 3.5.1.78) | protein | 589 | 26% helix, 28% strand | P0AES0 |
Ligands and binding sites
- GGA · D-gamma-glutamyl-N-{[(R)-{4-[(4-aminobutyl)amino]butyl}(phosphonooxy)phosphoryl]methyl}-D-alaninamide · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.82 | 0.88 | 76 | MG, GGA, ADP |
| 2 | 571 | 0.82 | 0.87 | 70 | MG, GGA, ADP |
| 3 | 802 | 0.77 | 0.81 | 90 | empty |
| 4 | 690 | 0.77 | 0.82 | 49 | empty |
| 5 | 579 | 0.75 | 0.82 | 66 | empty |
Interfaces
1 interface between chains.
- A–B · 1606 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2IOA · E. coli Bifunctional glutathionylspermidine synthetase/amidase Incomplex with Mg2+ and… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AES0 · AlphaFold monomer V2.0 prediction for bifunctional glutathionylspermidine… · a predicted model of the same protein · chain B 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 P0AES0
- Elsewhere: RCSB PDB 2IOA · PDBe 2IOA · UniProt P0AES0
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