11CF | pdb_000011cf

CHAP domain of Staphylococcus aureus-specific lysin L1

PDB DOI: https://doi.org/10.2210/pdb11CF/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.199 (Depositor), 0.209 (DCC)
R-Value Work:
0.187 (Depositor), 0.196 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 11CF

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 66.77 kDa
Atom Count: 5,171
Modeled Residue Count: 564
Deposited Residue Count: 584
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cell wall hydrolase LytN	A, B, C, D	146	Staphylococcus aureus	Mutation(s): 0 Gene Names: lytN, SAR1223 EC: 3
UniProt
Find proteins for Q9ZNI1 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q9ZNI1 Go to UniProtKB: Q9ZNI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZNI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A]	K [auth A] M [auth B] N [auth B] R [auth C] S [auth C] K [auth A], M [auth B], N [auth B], R [auth C], S [auth C], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], O [auth C], P [auth C], Q [auth C], T [auth D], U [auth D], V [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.199 (Depositor), 0.209 (DCC)
R-Value Work: 0.187 (Depositor), 0.196 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.12	α = 86.07
b = 57.43	β = 85.22
c = 63.05	γ = 83.99

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

Palowitch, G.M.

Dulberger, C.L.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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