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 v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Virulence protein vsde
UniProt: P0A2N2
Ligands: NA, CL
Pockets: 3 · best druggability 0.40

Structure

x-ray diffraction · 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.

Pocket	Volume (Å³)	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

5LQ7 · Salmonella effector SpvD - G161 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 5LQ7 · PDBe 5LQ7 · UniProt P0A2N2

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