6CIW | pdb_00006ciw

Hen Egg White Lysozyme Cocrystallized with 1,3-Di(2-pyridyl)propane

PDB DOI: https://doi.org/10.2210/pdb6CIW/pdb

Classification: Hydrolase/Inhibitor
Organism(s): Gallus gallus
Expression System: Gallus gallus
Mutation(s): No

Deposited: 2018-02-25 Released: 2019-01-02
Deposition Author(s): Morris, D.M., Ziegler, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.276 (Depositor), 0.282 (DCC)
R-Value Work:
0.240 (Depositor), 0.246 (DCC)
R-Value Observed:
0.242 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Inhibition of lysozyme's polymerization activity using a polymer structural mimic

Morris, D.L., Leeper, T.C., Ziegler, C.J.

(2018) Polym Chem 9: 3705-3708

DOI: https://doi.org/10.1039/C8PY00545A

Macromolecule Content

Total Structure Weight: 14.53 kDa
Atom Count: 1,063
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F44 (Subject of Investigation/LOI) Query on F44 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2,2'-(propane-1,3-diyl)dipyridine C₁₃ H₁₄ N₂ UHPWYBATPHCMGD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.276 (Depositor), 0.282 (DCC)
R-Value Work: 0.240 (Depositor), 0.246 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.874	α = 90
b = 76.874	β = 90
c = 37.249	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-01-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-01-02
Type: Initial release
Version 1.1: 2019-01-09
Changes: Data collection, Database references
Version 1.2: 2024-11-06
Changes: Data collection, Database references, 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.