4XYY

Hen Egg-White Lysozyme (HEWL) complexed with Zr(IV)-substituted Keggin-type polyoxometalate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Characterization of the Complex between Hen Egg-White Lysozyme and Zr(IV) -Substituted Keggin Polyoxometalate as Artificial Protease.

Sap, A.De Zitter, E.Van Meervelt, L.Parac-Vogt, T.N.

(2015) Chemistry 21: 11692-11695

  • DOI: 10.1002/chem.201501998

  • PubMed Abstract: 
  • Successful co-crystallization of a noncovalent complex between hen egg-white lysozyme (HEWL) and the monomeric Zr(IV) -substituted Keggin polyoxometalate (POM) (Zr1 K1), (Et2 NH2)3 [Zr(PW11 O39)] (1), has been achieved, and its single-crystal X-ray s ...

    Successful co-crystallization of a noncovalent complex between hen egg-white lysozyme (HEWL) and the monomeric Zr(IV) -substituted Keggin polyoxometalate (POM) (Zr1 K1), (Et2 NH2)3 [Zr(PW11 O39)] (1), has been achieved, and its single-crystal X-ray structure has been determined. The dimeric Zr(IV) -substituted Keggin-type polyoxometalate (Zr1 K2), (Et2 NH2)10 [Zr(PW11 O39 )2] (2), has been previously shown to exhibit remarkable selectivity towards HEWL hydrolysis. The reported X-ray structure shows that the hydrolytically active Zr(IV) -substituted Keggin POM exists as a monomeric species. Prior to hydrolysis, this monomer interacts with HEWL in the vicinity of the previously identified cleavage sites found at Trp28-Val29 and Asn44-Arg45, through water-mediated H-bonding and electrostatic interactions. Three binding sites are observed at the interface of the negatively charged Keggin POM and the positively charged regions of HEWL at: 1) Gly16, Tyr20, and Arg21; 2) Asn44, Arg45, and Asn46; and 3) Arg128.


    Organizational Affiliation

    Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001 Leuven, Heverlee (Belgium).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZKG
Query on ZKG

Download SDF File 
Download CCD File 
A
ZIRCONIUM(IV) PHOSPHOTUNGSTATE KEGGIN
O39 P W11 Zr
NBVITJPYFSGCOJ-UHFFFAOYSA-N
 Ligand Interaction
EDN
Query on EDN

Download SDF File 
Download CCD File 
A
ETHANE-1,2-DIAMINE
ETHYLENEDIAMINE
C2 H8 N2
PIICEJLVQHRZGT-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.232α = 90.00
b = 77.232β = 90.00
c = 37.961γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references