9QRS | pdb_00009qrs

Crystal structure of CERK6 extracellular domain

• PDB DOI: https://doi.org/10.2210/pdb9QRS/pdb

• Classification: PLANT PROTEIN
• Organism(s): Lotus japonicus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-04-04 Released: 2025-07-16 
• Deposition Author(s): Cheng, J.X.J., Gysel, K., Stougaard, J., Andersen, K.R.
• Funding Organization(s): Danish National Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Structural basis for size-selective perception of chitin in plants

Gysel, K., Hansen, S.B., Ruebsam, H., Alsarraf, H.M.A.B., Madland, E., Cheng, J.X.J., Baadegaard, C., Poulsen, E.C., Vinther, M., Fort, S., Stougaard, J., Andersen, K.R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.16 kDa 
• Atom Count: 3,705 
• Modeled Residue Count: 397 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysM type receptor kinase	A, B	204	Lotus japonicus	Mutation(s): 0  Gene Names: LYS6 EC: 2.7.11.1
UniProt
Find proteins for D3KTZ6 (Lotus japonicus) Explore D3KTZ6  Go to UniProtKB:  D3KTZ6
Glycosylation
Glycosylation Sites: 5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42466VF GlyCosmos:  G42466VF GlyGen:  G42466VF

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G44266EX GlyCosmos:  G44266EX GlyGen:  G44266EX

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	L [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
EDO	K [auth A], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.29	α = 90
b = 131.58	β = 108.137
c = 53.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Cheng, J.X.J., Gysel, K., Stougaard, J., Andersen, K.R.

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Funding Organization	Location	Grant Number
Danish National Research Foundation	Denmark	DNRF79

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release