11CH | pdb_000011ch

CHAP domain of Staphylococcus aureus-specific lysin L1 covalently complexed to Pep1a-CMK substrate mimic

PDB DOI: https://doi.org/10.2210/pdb11CH/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: 1.09 Å
R-Value Free:
0.252 (Depositor), 0.257 (DCC)
R-Value Work:
0.231 (Depositor), 0.237 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 17.62 kDa
Atom Count: 1,376
Modeled Residue Count: 142
Deposited Residue Count: 146
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cell wall hydrolase LytN	A	146	Staphylococcus aureus	Mutation(s): 0 Gene Names: lytN, SAR1223 EC: 3
UniProt
Find proteins for Q6GHI8 (Staphylococcus aureus (strain MRSA252)) Explore Q6GHI8 Go to UniProtKB: Q6GHI8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GHI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1DEZ (Subject of Investigation/LOI) Query on A1DEZ 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]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth A] C [auth A], D [auth A], E [auth A], F [auth A], H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A]