6HY6 | pdb_00006hy6

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

PDB DOI: https://doi.org/10.2210/pdb6HY6/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: 1.87 Å
R-Value Free:
0.192 (Depositor), 0.184 (DCC)
R-Value Work:
0.162 (Depositor), 0.163 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 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: 18.48 kDa
Atom Count: 1,138
Modeled Residue Count: 128
Deposited Residue Count: 128
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A [auth B]	128	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GXZ Query on GXZ Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	Ni(II)-substituted Wells-Dawson H₂ Ni O₆₁ P₂ W₁₇ HLPLUIGJBNKVKD-UHFFFAOYSA-A		Interactions Focus chain B Interactions & Density Focus chain B
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.192 (Depositor), 0.184 (DCC)
R-Value Work: 0.162 (Depositor), 0.163 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.937	α = 90
b = 78.937	β = 90
c = 37.272	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-10-01
Changes: Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.