6ZXQ

Adenylosuccinate Synthetase from H. pylori in complex with HDA, GDP, IMO, Mg

• PDB DOI: https://doi.org/10.2210/pdb6ZXQ/pdb

• Classification: LIGASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-07-30 Released: 2021-08-11 
• Deposition Author(s): Bubic, A., Stefanic, Z.
• Funding Organization(s): Croatian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.193 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

Starting Model: experimental

Literature

The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site

Bubic, A., Narczyk, M., Petek, A., Wojtys, M.I., Maksymiuk, W., Wielgus-Kutrowska, B., Winiewska-Szajewska, M., Pavkov-Keller, T., Bertosa, B., Stefanic, Z., Luic, M., Bzowska, A., Lescic Asler, I.

(2023) Int J Biol Macromol 

• DOI: https://doi.org/10.1016/j.ijbiomac.2022.12.001

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)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 47.9 kDa 
• Atom Count: 3,716 
• Modelled Residue Count: 410 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate synthetase	A	419	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: purA, HP_0255 EC: 6.3.4.4
UniProt
Find proteins for P56137 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56137  Go to UniProtKB:  P56137

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
IMO (Subject of Investigation/LOI)	D [auth A]	6-O-PHOSPHORYL INOSINE MONOPHOSPHATE C10 H14 N4 O11 P2 RXRZOKQPANIEDW-KQYNXXCUSA-N
HDA (Subject of Investigation/LOI)	B [auth A]	HADACIDIN C3 H5 N O4 URJHVPKUWOUENU-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.193 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.706	α = 90
b = 68.362	β = 121.11
c = 68.828	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Bubic, A., Stefanic, Z.

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Funding Organization	Location	Grant Number
Croatian Science Foundation	Croatia	--

Revision History  

• Version 1.0: 2021-08-11
  Type: Initial release
  
• Version 1.1: 2023-02-22
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description