MolNFT v1 · #40336 · protein
E. COLI bifunctional glutathionylspermidine SYNTHETASE/AMIDASE incomplex with MG2+ ,gsh and ADP
2IO9: “E. COLI bifunctional glutathionylspermidine SYNTHETASE/AMIDASE incomplex with MG2+ ,gsh and ADP”. X-ray diffraction, 3 ligands (ADP, GSH, MG), 14 pockets (best druggability 0.82). MolNFT v1 #40336 on GenesisL1: 3D structure, binding…
- PDB
- 2IO9
- Type
- protein
- Length
- 1,204 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
- ADP, GSH, MG
- Pockets
- 14 · 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 | 601 | 27% helix, 28% strand | P0AES0 |
| B | Bifunctional glutathionylspermidine SYNTHETASE/AMIDASE (EC 6.3.1.8, 3.5.1.78) | protein | 603 | 25% helix, 28% strand | P0AES0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GSH · Glutathione · 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
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.82 | 0.87 | 71 | MG, ADP, GSH |
| 2 | 600 | 0.82 | 0.87 | 81 | MG, ADP, GSH |
| 3 | 1039 | 0.80 | 0.81 | 82 | empty |
| 4 | 799 | 0.77 | 0.81 | 91 | empty |
| 5 | 605 | 0.74 | 0.81 | 70 | empty |
Interfaces
1 interface between chains.
- A–B · 1816 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2IO9 · E. coli Bifunctional glutathionylspermidine synthetase/amidase Incomplex with Mg2+ ,GSH… · 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 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 P0AES0
- Elsewhere: RCSB PDB 2IO9 · PDBe 2IO9 · UniProt P0AES0
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