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Crystal structure of the helicobacter pylori vacuolating toxin P55 domain

Analyse Crystal structure of the helicobacter pylori vacuolating toxin P55 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QV3
Type: protein
Length: 447 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolating cytotoxin
UniProt: Q48245
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolating cytotoxin	protein	447	7% helix, 51% strand	Q48245

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	145	0.53	0.80	22	empty
2	116	0.41	0.76	22	empty
3	81	0.40	0.79	20	empty
4	55	0.38	0.80	16	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2QV3 · Crystal Structure of the Helicobacter pylori Vacuolating Toxin p55 Domain · the same entry in another collection · chain A against A, TM-score 1.00
Q48245 · AlphaFold monomer V2.0 prediction for vacuolating cytotoxin autotransporter (Q48245) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q48245
Elsewhere: RCSB PDB 2QV3 · PDBe 2QV3 · UniProt Q48245

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