9XUA | pdb_00009xua

Hen Egg-White Lysozyme (HEWL) complexed with Caffeine

• PDB DOI: https://doi.org/10.2210/pdb9XUA/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2025-11-24 Released: 2025-12-10 
• Deposition Author(s): Roy, A., Khanppnavar, B., Dolui, S., Chakraborty, B., Datta, S., Maiti, N.C.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Hen Egg-White Lysozyme (HEWL) complexed with Caffeine

Roy, A., Khanppnavar, B., Dolui, S., Chakraborty, B., Datta, S., Maiti, N.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 14.62 kDa 
• Atom Count: 1,355 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CFF (Subject of Investigation/LOI)	F [auth A]	CAFFEINE C8 H10 N4 O2 RYYVLZVUVIJVGH-UHFFFAOYSA-N
NA	B [auth A], C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.687	α = 90
b = 78.687	β = 90
c = 37.113	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Roy, A., Khanppnavar, B., Dolui, S., Chakraborty, B., Datta, S., Maiti, N.C.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release