5EUF

The crystal structure of a protease from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb5EUF/pdb

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-18 Released: 2015-12-02 
• Deposition Author(s): Tan, K., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

The crystal structure of a protease from Helicobacter pylori

Tan, K., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 96.39 kDa 
• Atom Count: 6,521 
• Modelled Residue Count: 829 
• Deposited Residue Count: 838 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	419	Helicobacter pylori	Mutation(s): 0  Gene Names: pqqE, HPHPH19_0674 EC: 3.4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m35euf

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.159	α = 90
b = 50.266	β = 94.86
c = 147.889	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Tan, K., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2015-12-09
  Changes: Database references, Structure summary
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary