6HY8 | pdb_00006hy8

Cu(II)-substituted Wells-Dawson binding to Hen Egg-White Lysozyme (HEWL)

• PDB DOI: https://doi.org/10.2210/pdb6HY8/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2018-10-19 Released: 2019-10-30 
• Deposition Author(s): Vandebroek, L., Van Meervelt, L., Parac-Vogt, T.N.
• Funding Organization(s): Research Foundation - Flanders

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Noncovalent Complexes Formed between Metal-Substituted Polyoxometalates and Hen Egg White Lysozyme

Vandebroek, L., Mampaey, Y., Antonyuk, S., Van Meervelt, L., Parac-Vogt, T.N.

(2019) Eur J Inorg Chem 

• DOI: https://doi.org/10.1002/ejic.201801113

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.73 kDa 
• Atom Count: 1,306 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GXW	B [auth A]	Cu(II)-substituted Wells-Dawson Cu H2 O61 P2 W17 FJYYOMDTXNHMAS-UHFFFAOYSA-A
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.841	α = 90
b = 78.841	β = 90
c = 37.193	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Vandebroek, L., Van Meervelt, L., Parac-Vogt, T.N.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	--

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary