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

Starting Model: experimental
View more details

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