6MX9 | pdb_00006mx9

Lysozyme bound to 3-Aminophenol

• PDB DOI: https://doi.org/10.2210/pdb6MX9/pdb

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


• Deposited: 2018-10-30 Released: 2018-12-26 
• Deposition Author(s): Blackburn, A., Partowmah, S.H., Brennan, H.M., Mestizo, K.E., Stivala, C.D., Petreczky, J., Perez, A., Horn, A., McSweeney, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.186 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

A simple technique to improve microcrystals using gel exclusion of nucleation inducing elements

Blackburn, A., Partowmah, S.H., Brennan, H.M., Mestizo, K.E., Stivala, C.D., Petreczky, J., Perez, A., Horn, A., McSweeney, S.

To be published.

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: 14.95 kDa 
• Atom Count: 1,342 
• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	J [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
K5V (Subject of Investigation/LOI)	K [auth A], L [auth A]	3-aminophenol C6 H7 N O CWLKGDAVCFYWJK-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.186 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.085	α = 90
b = 80.085	β = 90
c = 37.197	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Blackburn, A., Partowmah, S.H., Brennan, H.M., Mestizo, K.E., Stivala, C.D., Petreczky, J., Perez, A., Horn, A., McSweeney, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM111244
Department of Energy (DOE, United States)	United States	KP1605010

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary