5O6Y

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


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
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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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan N-acetylglucosamine deacetylase214Bacillus cereus ATCC 14579Mutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81EK9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan N-acetylglucosamine deacetylase
B, C, D
214Bacillus cereus ATCC 14579Mutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81EK9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE3
Query on PE3

Download Ideal Coordinates CCD File 
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
Query on 5YA

Download Ideal Coordinates CCD File 
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
Query on PG0

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M [auth A]2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG
Query on PEG

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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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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
DMS
Query on DMS

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Y [auth B],
Z [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

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DB [auth D],
IB [auth D],
TA [auth C],
X [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

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JB [auth D],
MA [auth B],
NA [auth B],
U [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PXU
Query on PXU
B, C, D
L-PEPTIDE LINKINGC5 H9 N O3PRO
Binding Affinity Annotations 
IDSourceBinding 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 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.042α = 90
b = 93.042β = 90
c = 243.868γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionInnovCrete

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