8WEC

Crystal structure of Arabidopsis thaliana MIK2 ectodomain in complex with BAK1 ectodomain and SCOOP12

PDB DOI: https://doi.org/10.2210/pdb8WEC/pdb

Classification: PLANT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2023-09-17 Released: 2024-11-06
Deposition Author(s): Wan, L.H., Hu, Y.X., Wu, H.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.256
R-Value Work: 0.245
R-Value Observed: 0.245

Starting Model: in silico
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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

Mechanistic study of SCOOPs recognition by MIK2-BAK1 complex reveals the role of N-glycans in plant ligand-receptor-coreceptor complex formation

Hu, Y.X., Wu, H.M.

(2024) Nature Plants

DOI: https://doi.org/10.1038/s41477-024-01836-3

Macromolecule Content

Total Structure Weight: 213.95 kDa
Atom Count: 13,386
Modelled Residue Count: 1,649
Deposited Residue Count: 1,852
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MDIS1-interacting receptor like kinase 2	A, D	683	Arabidopsis thaliana	Mutation(s): 3 Gene Names: MIK2, At4g08850, T32A17.160 EC: 2.7.11.1
UniProt
Find proteins for Q8VZG8 (Arabidopsis thaliana) Explore Q8VZG8 Go to UniProtKB: Q8VZG8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VZG8
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain A Focus chain D
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1	B, E	230	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BAK1, ELG, SERK3, At4g33430, F17M5.190 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q94F62 (Arabidopsis thaliana) Explore Q94F62 Go to UniProtKB: Q94F62
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q94F62
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE-RICH ENDOGENOUS PEPTIDE (SCOOP)	C, F	13	Arabidopsis thaliana	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, J, K, L G, I, J, K, L, Q, R, S, W	2		N-Glycosylation	Interactions Focus chain G Focus chain I Focus chain J Focus chain K Focus chain L Focus chain Q Focus chain R Focus chain S Focus chain W Interactions & Density Focus chain G Focus chain I Focus chain J Focus chain K Focus chain L Focus chain Q Focus chain R Focus chain S Focus chain W
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	4		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G63564LA GlyCosmos: G63564LA

Entity ID: 6
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	M, O	3		N-Glycosylation	Interactions Focus chain M Focus chain O Interactions & Density Focus chain M Focus chain O
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N, T	3		N-Glycosylation	Interactions Focus chain N Focus chain T Interactions & Density Focus chain N Focus chain T
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose	P	2		N/A	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G07696MJ GlyCosmos: G07696MJ GlyGen: G07696MJ

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	U, V	2		N-Glycosylation	Interactions Focus chain U Focus chain V Interactions & Density Focus chain U Focus chain V
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 2 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 BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] FA [auth D] BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
BMA (Subject of Investigation/LOI) Query on BMA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain AA [auth B]	AA [auth B]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]