7E69 | pdb_00007e69

The crystal structure of peptidoglycan peptidase in complex with inhibitor 3-3

PDB DOI: https://doi.org/10.2210/pdb7E69/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-02-21 Released: 2022-02-23
Deposition Author(s): Choi, Y., Min, K.J., Yoon, H.J., Lee, H.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.231 (Depositor), 0.230 (DCC)
R-Value Work:
0.170 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-based inhibitor design for reshaping bacterial morphology

Choi, Y., Park, J.S., Kim, J., Min, K., Mahasenan, K., Kim, C., Yoon, H.J., Lim, S., Cheon, D.H., Lee, Y., Ryu, S., Mobashery, S., Kim, B.M., Lee, H.H.

(2022) Commun Biol 5: 395

DOI: https://doi.org/10.1038/s42003-022-03355-3

Macromolecule Content

Total Structure Weight: 28.84 kDa
Atom Count: 2,067
Modeled Residue Count: 255
Deposited Residue Count: 255
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M23	A	255	Campylobacter jejuni	Mutation(s): 1 Gene Names: A8118_01115
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HX6 (Subject of Investigation/LOI) Query on HX6 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]	N-oxidanyl-4-[(4-sulfamoylphenyl)methyl]benzamide C₁₄ H₁₄ N₂ O₄ S ZYVHYCNSGQRCBB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN (Subject of Investigation/LOI) Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.231 (Depositor), 0.230 (DCC)
R-Value Work: 0.170 (Depositor), 0.180 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.649	α = 90
b = 115.649	β = 90
c = 56.614	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-02-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-02-23
Type: Initial release
Version 1.1: 2022-08-31
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

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.