Research workbench
E. COLI bifunctional glutathionylspermidine SYNTHETASE/AMIDASE incomplex with MG2+ and ADP
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
- 2IO8
- Type
- protein
- Length
- 1,191 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
- CYS, ADP, MG
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional glutathionylspermidine SYNTHETASE/AMIDASE (EC 6.3.1.8, 3.5.1.78) | protein | 598 | 27% helix, 28% strand | P0AES0 |
| B | Bifunctional glutathionylspermidine SYNTHETASE/AMIDASE (EC 6.3.1.8, 3.5.1.78) | protein | 593 | 26% helix, 29% strand | P0AES0 |
Ligands and binding sites
- CYS · Cysteine · 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
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.82 | 0.88 | 73 | MG, CYS, ADP |
| 2 | 608 | 0.81 | 0.86 | 80 | MG, CYS, ADP |
| 3 | 651 | 0.76 | 0.82 | 47 | empty |
| 4 | 655 | 0.76 | 0.82 | 73 | empty |
| 5 | 628 | 0.75 | 0.82 | 76 | empty |
Interfaces
1 interface between chains.
- A–B · 1783 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2IO8 · E. coli Bifunctional glutathionylspermidine synthetase/amidase Incomplex with Mg2+ and ADP · the same entry in another collection · chain B against B, 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 2IO8 · PDBe 2IO8 · UniProt P0AES0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.