11CI | pdb_000011ci

Staphylococcus aureus-specific lysin L1-3 (LysM-CHAP) covalently complexed to Pep1a-CMK substrate mimic

• PDB DOI: https://doi.org/10.2210/pdb11CI/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-02-17 Released: 2026-05-06 
• Deposition Author(s): Miller, H.A., Palowitch, G.M., Dulberger, C.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.266 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Starting Models: experimental, in silico

Literature

Multi-dimensional optimization of a lysin towards a ribolysin against life-threatening S. aureus infections: Fc-LysM-CHAP and its strong synergy with standard of care antibiotics

Badarau, A., Bauer, B., Visram, Z., Qiao, R., Majoros-Hashempour, A., Sollner, J., Durica-Mitic, S., Dunne, O.M., Kluj, R., Kestemont, D., Kieninger, A.K., Kulig, M., Berdaguer, R., Schwebs, T., Zerbs, M., Czermak, P., von Freyberg, M., Schmidt, J., Schmidberger, L., Mayer, D., Protano, M., Miller, H.A., Palowitch, G.M., Dulberger, C.L., Massaro, M., Ivanisenko, N., Jacomet, H., Ngatcha Bakoue, D., Oteri, F., Sela, G., Corsini, L.

(2026) bioRxiv 

• DOI: https://doi.org/10.64898/2026.04.27.720530

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.09 kDa 
• Atom Count: 1,555 
• Modeled Residue Count: 189 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cell wall hydrolase LytN	A	215	Staphylococcus aureus	Mutation(s): 0  Gene Names: lytN, SAS1181 EC: 3
UniProt
Find proteins for Q6G9W6 (Staphylococcus aureus (strain MSSA476)) Explore Q6G9W6  Go to UniProtKB:  Q6G9W6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1DEZ (Subject of Investigation/LOI)	B [auth A]	N~2~-acetyl-N~6~-{(4M)-3-carboxy-4-[(10aR)-6-hydroxy-3-oxo-4,10a-dihydro-3H-xanthen-9-yl]benzene-1-carbonyl}-D-lysyl-L-alanyl-D-alpha-glutaminyl-N-[(2R)-3-oxobutan-2-yl]-L-lysinamide C47 H58 N8 O13 RSJHTSPAGHRDHK-KXOAOMPMSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.266 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.994	α = 90
b = 135.046	β = 90
c = 57.626	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Miller, H.A., Palowitch, G.M., Dulberger, C.L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release