Research workbench
Salmonella effector SpvD - G161 variant
Analyse Salmonella effector SpvD - G161 variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LQ7
- Type
- protein
- Length
- 206 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Salmonella enterica
- Molecule
- Virulence protein vsdE
- UniProt
- P0A2N2
- Ligands
- NA, CL
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virulence protein vsdE | protein | 206 | 35% helix, 20% strand | P0A2N2 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.40 | 0.78 | 21 | TRS |
| 2 | 71 | 0.31 | 0.75 | 15 | empty |
| 3 | 53 | 0.29 | 0.75 | 11 | empty |
Compared structures
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 P0A2N2
- Elsewhere: RCSB PDB 5LQ7 · PDBe 5LQ7 · UniProt P0A2N2
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