6BGE

HELICOBACTER PYLORI ATPASE, HP0525, IN COMPLEX WITH 1G2 COMPOUND

• PDB DOI: https://doi.org/10.2210/pdb6BGE/pdb

• Classification: ATP binding Protein
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-27 Released: 2018-10-31 
• Deposition Author(s): Arya, T., Casu, B., Baron, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.280 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

CagAlpha in complex with hexamer inhibitor

Arya, T., Casu, B., Baron, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 74.43 kDa 
• Atom Count: 5,222 
• Modelled Residue Count: 646 
• Deposited Residue Count: 646 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VirB11-like protein	A, B	323	Helicobacter pylori	Mutation(s): 0  Gene Names: HP0525, HPY1846_06315
UniProt
Find proteins for Q6VRM0 (Helicobacter pylori) Explore Q6VRM0  Go to UniProtKB:  Q6VRM0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
DN7	G [auth B]	4-[(pyridin-2-yl)oxy]benzoic acid C12 H9 N O3 GKSKQZLHPWBLJL-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.280 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.075	α = 90
b = 112.075	β = 90
c = 231.006	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Arya, T., Casu, B., Baron, C.

---

Funding Organization	Location	Grant Number
	Canada	--

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-12-27
  Changes: Structure summary