6ZXQ | pdb_00006zxq

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.193 (Depositor), 0.194 (DCC)
R-Value Work:
0.151 (Depositor), 0.153 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56137
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
IMO (Subject of Investigation/LOI) Query on IMO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	6-O-PHOSPHORYL INOSINE MONOPHOSPHATE C₁₀ H₁₄ N₄ O₁₁ P₂ RXRZOKQPANIEDW-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
HDA (Subject of Investigation/LOI) Query on HDA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	HADACIDIN C₃ H₅ N O₄ URJHVPKUWOUENU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.193 (Depositor), 0.194 (DCC)
R-Value Work: 0.151 (Depositor), 0.153 (DCC)
R-Value Observed: 0.152 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Croatian Science Foundation	Croatia	--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.