5O6Y | pdb_00005o6y

Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide

• PDB DOI: https://doi.org/10.2210/pdb5O6Y/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-06-07 Released: 2018-06-20 
• Deposition Author(s): Fadouloglou, V.E., Kotsifaki, D., Kokkinidis, M.
• Funding Organization(s): European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide

Fadouloglou, V.E., Kotsifaki, D., Kokkinidis, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 102.51 kDa 
• Atom Count: 7,815 
• Modeled Residue Count: 856 
• Deposited Residue Count: 856 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan N-acetylglucosamine deacetylase	A	214	Bacillus cereus ATCC 14579	Mutation(s): 0  Gene Names: BC_1960 EC: 3.5.1 (PDB Primary Data), 3.5.1.104 (UniProt)
UniProt
Find proteins for Q81EK9 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81EK9  Go to UniProtKB:  Q81EK9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan N-acetylglucosamine deacetylase	B, C, D	214	Bacillus cereus ATCC 14579	Mutation(s): 0  Gene Names: BC_1960 EC: 3.5.1 (PDB Primary Data), 3.5.1.104 (UniProt)
UniProt
Find proteins for Q81EK9 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81EK9  Go to UniProtKB:  Q81EK9

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE3	I [auth A], UA [auth C]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N
5YA	CB [auth D], H [auth A], SA [auth C], W [auth B]	4-naphthalen-1-yl-~{N}-oxidanyl-benzamide C17 H13 N O2 PKQVYJOPUCLLCD-UHFFFAOYSA-N
PG0	M [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG	AA [auth B], BA [auth B], CA [auth B], EB [auth D], FB [auth D], GB [auth D], J [auth A], K [auth A], L [auth A], VA [auth C], WA [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	BB [auth D], E [auth A], F [auth A], G [auth A], OA [auth C], PA [auth C], QA [auth C], RA [auth C], V [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	DB [auth D], IB [auth D], TA [auth C], X [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	JB [auth D], MA [auth B], NA [auth B], U [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	AB [auth C], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], HB [auth D], IA [auth B], JA [auth B], KA [auth B], LA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], XA [auth C], YA [auth C], ZA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PXU	B, C, D	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Binding Affinity Annotations
ID	Source	Binding Affinity
5YA	BindingDB:  5O6Y	Ki: 6.60e+4 (nM) from 1 assay(s)
		IC50: 1.32e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.042	α = 90
b = 93.042	β = 90
c = 243.868	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Fadouloglou, V.E., Kotsifaki, D., Kokkinidis, M.

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Funding Organization	Location	Grant Number
European Union		InnovCrete

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description