6BGE | pdb_00006bge

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 (Depositor), 0.280 (DCC)
R-Value Work:
0.223 (Depositor), 0.229 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

CagAlpha in complex with hexamer inhibitor

Arya, T., Casu, B., Baron, C.

To be published.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6VRM0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DN7 Query on DN7 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	4-[(pyridin-2-yl)oxy]benzoic acid C₁₂ H₉ N O₃ GKSKQZLHPWBLJL-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.280 (Depositor), 0.280 (DCC)
R-Value Work: 0.223 (Depositor), 0.229 (DCC)
R-Value Observed: 0.226 (Depositor)

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

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Ligand Structure Quality Assessment

View more in-depth experimental data

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 (Full details and data files)

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

6BGE | pdb_00006bge

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

Literature

CagAlpha in complex with hexamer inhibitor

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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