Research workbench
Crystal structure of SdoA from Pseudomonas putida in complex with glutathione
Analyse Crystal structure of SdoA from Pseudomonas putida in complex with glutathione in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YSL
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4618
- Source
- Pseudomonas putida (strain F1 / ATCC 700007)
- Molecule
- Beta-lactamase domain protein
- UniProt
- A5VWI3
- Ligands
- GSH, FE
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · resolution 1.4618 · 1 distinct chain · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase domain protein | protein | 294 | 24% helix, 28% strand | A5VWI3 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.62 | 0.90 | 17 | empty |
| 2 | 215 | 0.55 | 0.78 | 38 | FE, GSH |
| 3 | 191 | 0.51 | 0.77 | 27 | FE, GSH |
| 4 | 115 | 0.50 | 0.80 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1411 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4YSL · Crystal structure of sdoa from pseudomonas putida in complex with glutathione · 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 A5VWI3
- Elsewhere: RCSB PDB 4YSL · PDBe 4YSL · UniProt A5VWI3
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