6HY4

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

PDB DOI: https://doi.org/10.2210/pdb6HY4/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.214
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 18.55 kDa
Atom Count: 1,143
Modelled Residue Count: 128
Deposited Residue Count: 128
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	128	Gallus gallus	Mutation(s): 0 Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CWO Query on CWO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	Co(II)-substituted Wells-Dawson Co H₂ O₆₁ P₂ W₁₇ MRXRADKQNKKZNK-UHFFFAOYSA-A		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.214
R-Value Work: 0.177
R-Value Observed: 0.179
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.734	α = 90
b = 78.734	β = 90
c = 37.179	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-10-30

Deposition Author(s):

Van Meervelt, L.

Parac-Vogt, T.N.

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

Revision History (Full details and data files)

Version 1.0: 2019-10-30
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.