9F65 | pdb_00009f65

Crystal structure of thiol peroxidase mutant (C94A) in complex with Metro-P3* (H. pylori)

PDB DOI: https://doi.org/10.2210/pdb9F65/pdb

Classification: OXIDOREDUCTASE
Organism(s): Helicobacter pylori
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-04-30 Released: 2025-05-14
Deposition Author(s): Fiedler, M.K., Gong, R., Fuchs, S., Rox, K., Friedrich, V., Pfeiffer, D., Reinhardt, T., Mibus, C., Huber, M., Hess, C., Mejias-Luque, R., Gerhard, M., Groll, M., Sieber, S.A.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 ?
R-Value Free:
0.217 (Depositor), 0.223 (DCC)
R-Value Work:
0.177 (Depositor), 0.183 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

5-Nitroimidazole ethers boost anti-Helicobacter pylori activity via a dual mode of action and effectively eradicate infections in vivo

Fiedler, M.K., Gong, R., Fuchs, S., Rox, K., Friedrich, V., Pfeiffer, D., Reinhardt, T., Mibus, C., Huber, M., Hess, C., Mejias-Luque, R., Gerhard, M., Groll, M., Sieber, S.A.

To be published.

Macromolecule Content

Total Structure Weight: 41.58 kDa
Atom Count: 2,588
Modelled Residue Count: 330
Deposited Residue Count: 376
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol peroxidase	A, B	188	Helicobacter pylori	Mutation(s): 1 Gene Names: tpx, HP_0390 EC: 1.11.1.24
UniProt
Find proteins for O25151 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25151 Go to UniProtKB: O25151
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O25151
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IAR (Subject of Investigation/LOI) Query on A1IAR 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]	3-methyl-2-(prop-2-ynoxymethyl)imidazol-4-amine C₈ H₁₁ N₃ O JGQPVNNBPSNUGF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 ?
R-Value Free: 0.217 (Depositor), 0.223 (DCC)
R-Value Work: 0.177 (Depositor), 0.183 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 40.57	α = 90
b = 67.76	β = 98.7
c = 64.03	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Mejias-Luque, R.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1309 - 325871075

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release

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.