5O6Y

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.254
R-Value Work: 0.196
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q81EK9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q81EK9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain UA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain UA [auth C]	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		Interactions Focus chain I [auth A] Focus chain UA [auth C] Interactions & Density Focus chain I [auth A] Focus chain UA [auth C]
5YA Query on 5YA Download Ideal Coordinates CCD File SDF format, chain CB [auth D] SDF format, chain H [auth A] SDF format, chain SA [auth C] SDF format, chain W [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain W [auth B]	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		Interactions Focus chain CB [auth D] Focus chain H [auth A] Focus chain SA [auth C] Focus chain W [auth B] Interactions & Density Focus chain CB [auth D] Focus chain H [auth A] Focus chain SA [auth C] Focus chain W [auth B]
PG0 Query on PG0 Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain VA [auth C] SDF format, chain WA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C]	AA [auth B] BA [auth B] CA [auth B] EB [auth D] FB [auth D] 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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain VA [auth C] Focus chain WA [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain V [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain V [auth B]	BB [auth D] E [auth A] F [auth A] G [auth A] OA [auth C] 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		Interactions Focus chain BB [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain V [auth B] Interactions & Density Focus chain BB [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain V [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain DB [auth D] SDF format, chain IB [auth D] SDF format, chain TA [auth C] SDF format, chain X [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain TA [auth C] MOL2 format, chain X [auth B]	DB [auth D], IB [auth D], TA [auth C], X [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DB [auth D] Focus chain IB [auth D] Focus chain TA [auth C] Focus chain X [auth B] Interactions & Density Focus chain DB [auth D] Focus chain IB [auth D] Focus chain TA [auth C] Focus chain X [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain JB [auth D] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain U [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain U [auth A]	JB [auth D], MA [auth B], NA [auth B], U [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain JB [auth D] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain U [auth A] Interactions & Density Focus chain JB [auth D] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain U [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C]	AB [auth C] DA [auth B] EA [auth B] FA [auth B] GA [auth B] 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		Interactions Focus chain AB [auth C] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PXU Query on 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)
5YA	BindingDB: 5O6Y	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
R-Value Work: 0.196
R-Value Observed: 0.199
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Fadouloglou, V.E.

Kotsifaki, D.

Kokkinidis, M.

Funding Organization	Location	Grant Number
European Union		InnovCrete

Revision History (Full details and data files)

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