7E64

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidase M23255Campylobacter jejuniMutation(s): 1 
Gene Names: A8118_01115
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HWX (Subject of Investigation/LOI)
Query on HWX

Download Ideal Coordinates CCD File 
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
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.14α = 90
b = 116.14β = 90
c = 57.82γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2015R1A5A1008958

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