7E64 | pdb_00007e64

The crystal structure of peptidoglycan peptidase in complex with inhibitor 2-2

PDB DOI: https://doi.org/10.2210/pdb7E64/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.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.232 (Depositor), 0.231 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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: 28.83 kDa
Atom Count: 2,036
Modeled Residue Count: 255
Deposited Residue Count: 255
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M23	A	255	Campylobacter jejuni	Mutation(s): 1 Gene Names: A8118_01115

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HWX (Subject of Investigation/LOI) Query on HWX 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]	2-[[(3S)-3-acetamido-4-[[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]amino]ethanoic acid C₁₁ H₂₀ N₄ O₆ SPJUSNPGUPFCMZ-SVRRBLITSA-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: 2.90 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.232 (Depositor), 0.231 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.14	α = 90
b = 116.14	β = 90
c = 57.82	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2015R1A5A1008958

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

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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.