Research workbench

Salmonella effector spvd - R161 variant

Analyse Salmonella effector spvd - R161 variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LQ6
Type: protein
Length: 184 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Virulence protein vsde
UniProt: P0A2N2
Ligands: NA
Pockets: 2 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Virulence protein vsde	protein	184	41% helix, 22% strand	P0A2N2

Ligands and binding sites

NA · Sodium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.31	0.74	15	empty
2	55	0.30	0.76	12	empty

Compared structures

5LQ6 · Salmonella effector SpvD - R161 variant · the same entry in another collection · chain A against A, TM-score 1.00
P0A2N2 · AlphaFold monomer V2.0 prediction for virulence protein vsde (P0A2N2) · 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 P0A2N2
Elsewhere: RCSB PDB 5LQ6 · PDBe 5LQ6 · UniProt P0A2N2

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