9WGK | pdb_00009wgk

Crystal structure of OcuKAI2d2 from Orobanche cumana bound to Dehydrocostus Lactone

• PDB DOI: https://doi.org/10.2210/pdb9WGK/pdb

• Classification: HYDROLASE
• Organism(s): Orobanche cernua var. cumana
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-08-24 Released: 2026-05-20 
• Deposition Author(s): Hameed, U.F.S., Arold, S.T.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.237 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Orobanche cumana KAI2d2 mediates perception of dehydrocostus lactone and strigolactones and is inhibited by triazole ureas.

Shahul Hameed, U.F., Jamil, M., Zarban, R., Saito, Y., Alashoor, K., Balakrishna, A., Asami, T., Arold, S.T., Al-Babili, S.

(2026) Plant Commun : 101889-101889

• PubMed: 42104616 
• DOI: https://doi.org/10.1016/j.xplc.2026.101889
• Primary Citation Related Structures: 
  9WGK, 9WGM, 9WGN, 9WGO, 9WGQ


• PubMed Abstract: 
  

  Seed germination of the parasitic plant Orobanche cumana is induced by host-derived strigolactones and dehydrocostus lactone. We show that the KAI2d2 receptor perceives both ligands through distinct modes of interaction. Triazole urea compounds covalently inhibit KAI2d receptors, suppressing germination without affecting sunflower growth.

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Organizational Affiliation: 
• KAUST Center of Excellence for Smart Health, Division of Biomedical Sciences, King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
The Bioactives Laboratory, KAUST Center of Excellence for Food Security, King Abdullah University of Science and Technology, Saudi Arabia.
The Bioactives Laboratory, KAUST Center of Excellence for Food Security, King Abdullah University of Science and Technology, Saudi Arabia; Department of Agricultural Biotechnology, King Faisal University, Saudi Arabia.
Marine Open Innovation (MaOI) Institute, 9-25 Hinodecho, Shimizu-ku, Shizuoka 424-0922, Japan.
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
KAUST Center of Excellence for Smart Health, Division of Biomedical Sciences, King Abdullah University of Science and Technology (KAUST), Saudi Arabia. Electronic address: [e-mail].
The Bioactives Laboratory, KAUST Center of Excellence for Food Security, King Abdullah University of Science and Technology, Saudi Arabia; The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Saudi Arabia; KAUST Center of Excellence for Sustainable Food Security, King Abdullah University of Science and Technology (KAUST), Saudi Arabia. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.74 kDa 
• Atom Count: 2,131 
• Modeled Residue Count: 273 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OcuKAI2d2 protein	A	277	Orobanche cernua var. cumana	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1MBP (Subject of Investigation/LOI)	B [auth A]	(3~{a}~{R},6~{a}~{S},9~{a}~{R},9~{b}~{S})-3,6,9-trimethylidene-3~{a},4,5,6~{a},7,8,9~{a},9~{b}-octahydroazuleno[4,5-b]furan-2-one C15 H18 O2 NETSQGRTUNRXEO-MQYQWHSLSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.237 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.220 (DCC) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.84	α = 90
b = 150.84	β = 90
c = 57.6	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-20 
Deposition Author(s): Hameed, U.F.S., Arold, S.T.

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Funding Organization	Location	Grant Number
Other private	Saudi Arabia	King Abdullah University of Science and Technology

Revision History  

• Version 1.0: 2026-05-20
  Type: Initial release