9Q83 | pdb_00009q83

Crystal structure of Lotus japonicus CHIP13 in complex with chitooctaose

PDB DOI: https://doi.org/10.2210/pdb9Q83/pdb

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

Deposited: 2025-02-21 Released: 2025-07-16
Deposition Author(s): Gysel, K., Andersen, K.R.
Funding Organization(s): The Carlsberg Foundation, Danish Council for Independent Research, Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.243 (Depositor), 0.242 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

Macromolecule Content

Total Structure Weight: 61.83 kDa
Atom Count: 4,242
Modeled Residue Count: 437
Deposited Residue Count: 496
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysM type receptor kinase	A, B [auth E]	248	Lotus japonicus	Mutation(s): 0 Gene Names: LYS13
UniProt
Find proteins for D3KU00 (Lotus japonicus) Explore D3KU00 Go to UniProtKB: D3KU00
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3KU00
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B [auth E]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B], F	8		N/A	Interactions Focus chain C [auth B] Focus chain F Interactions & Density Focus chain C [auth B] Focus chain F
Glycosylation Resources
GlyTouCan: G83257UC GlyCosmos: G83257UC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C], G	3		N-Glycosylation	Interactions Focus chain D [auth C] Focus chain G Interactions & Density Focus chain D [auth C] Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D], H [auth I], J [auth K]	2		N-Glycosylation	Interactions Focus chain E [auth D] Focus chain H [auth I] Focus chain J [auth K] Interactions & Density Focus chain E [auth D] Focus chain H [auth I] Focus chain J [auth K]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth J], K [auth M]	3		N-Glycosylation	Interactions Focus chain I [auth J] Focus chain K [auth M] Interactions & Density Focus chain I [auth J] Focus chain K [auth M]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain R [auth E] MOL2 format, chain R [auth E] mmCIF format, chain R [auth E]	R [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain R [auth E] Interactions & Density Focus chain R [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth E]	P [auth E], Q [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth E] Focus chain Q [auth E] Interactions & Density Focus chain P [auth E] Focus chain Q [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	N [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]