4CT3

Methylmercury chloride derivative structure of the lytic CHAPK domain of the endolysin LysK from Staphylococcus aureus bacteriophage K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


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Literature

Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K.

Sanz-Gaitero, M.Keary, R.Garcia-Doval, C.Coffey, A.van Raaij, M.J.

(2014) Virol J 11: 133-133

  • DOI: 10.1186/1743-422X-11-133
  • Primary Citation of Related Structures:  
    4CSH, 4CT3

  • PubMed Abstract: 
  • Bacteriophages encode endolysins to lyse their host cell and allow escape of their progeny. Endolysins are also active against Gram-positive bacteria when applied from the outside and are thus attractive anti-bacterial agents. LysK, an endolysin from staphylococcal phage K, contains an N-terminal cysteine-histidine dependent amido-hydrolase/peptidase domain (CHAP(K)), a central amidase domain and a C-terminal SH3b cell wall-binding domain ...

    Bacteriophages encode endolysins to lyse their host cell and allow escape of their progeny. Endolysins are also active against Gram-positive bacteria when applied from the outside and are thus attractive anti-bacterial agents. LysK, an endolysin from staphylococcal phage K, contains an N-terminal cysteine-histidine dependent amido-hydrolase/peptidase domain (CHAP(K)), a central amidase domain and a C-terminal SH3b cell wall-binding domain. CHAP(K) cleaves bacterial peptidoglycan between the tetra-peptide stem and the penta-glycine bridge.


    Related Citations: 
    • Crystallization of the Chap Domain of the Endolysin from Staphylococcus Aureus Bacteriophage K.
      Sanz-Gaitero, M., Keary, R., Garcia-Doval, C., Coffey, A., van Raaij, M.J.
      (2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1393
    • In Silico Modeling of the Staphylococcal Bacteriophage-Derived Peptidase Chap(K).
      Fenton, M., Cooney, J.C., Ross, R.P., Sleator, R.D., McAuliffe, O., O'Mahony, J., Coffey, A.
      (2011) Bacteriophage 1: 198
    • Phage Lysin Lysk Can be Truncated to its Chap Domain and Retain Lytic Activity Against Live Antibiotic-Resistant Staphylococci.
      Horgan, M., O'Flynn, G., Garry, J., Cooney, J., Coffey, A., Fitzgerald, G.F., Ross, R.P., McAuliffe, O.
      (2009) Appl Environ Microbiol 75: 872

    Organizational Affiliation

    Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain. mjvanraaij@cnb.csic.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORF30/ORF32A, B, C, D165Staphylococcus virus KMutation(s): 0 
Gene Names: PhageK_071
UniProt
Find proteins for Q6Y7T6 (Staphylococcus phage K)
Explore Q6Y7T6 
Go to UniProtKB:  Q6Y7T6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6Y7T6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMH
Query on CMH

Download Ideal Coordinates CCD File 
BA [auth D],
E [auth A],
N [auth B],
V [auth C]
S-(METHYLMERCURY)-L-CYSTEINE
C4 H9 Hg N O2 S
OMYFBIZVJYGJJA-JIZZDEOASA-M
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
DA [auth D],
H [auth A],
P [auth B],
W [auth C]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
MMC
Query on MMC

Download Ideal Coordinates CCD File 
FA [auth D],
GA [auth D],
J [auth A],
K [auth A],
R [auth B],
FA [auth D],
GA [auth D],
J [auth A],
K [auth A],
R [auth B],
S [auth B],
Y [auth C],
Z [auth C]
METHYL MERCURY ION
C H3 Hg
DBUXSCUEGJMZAE-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download Ideal Coordinates CCD File 
AA [auth C],
HA [auth D],
L [auth A],
M [auth A],
T [auth B],
AA [auth C],
HA [auth D],
L [auth A],
M [auth A],
T [auth B],
U [auth B]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth D],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth D],
I [auth A],
Q [auth B],
X [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.02α = 91.8
b = 61.52β = 98.73
c = 72.8γ = 90.01
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Database references