3KB3

Crystal structure of abscisic acid-bound PYL2 in complex with HAB1

• PDB DOI: https://doi.org/10.2210/pdb3KB3/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-20 Released: 2009-12-08 
• Deposition Author(s): Zhou, X.E., Melcher, K., Soon, F.-F., Ng, L.-M., Xu, Y., Suino-Powell, K.M., Kovach, A., Li, J., Xu, H.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.259 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Agate-latch-lock mechanism for hormone signalling by abscisic acid receptors

Melcher, K., Ng, L.-M., Zhou, X.E., Soon, F.-F., Xu, Y., Suino-Powell, K.-M., Park, S.-Y., Weiner, J.J., Fujii, H., Chinnusamy, V., Kovach, A., Li, J., Wang, Y., Li, J.Y., Peterson, F.C., Jensen, D.R., Yong, E.-L., Volkman, B.F., Cutler, S.R., Zhu, J.-K., Xu, H.E.

(2009) Nature 462: 602-608

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 55.72 kDa 
• Atom Count: 3,933 
• Modelled Residue Count: 470 
• Deposited Residue Count: 497 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein At2g26040	A	176	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At2g26040
UniProt
Find proteins for O80992 (Arabidopsis thaliana) Explore O80992  Go to UniProtKB:  O80992

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein phosphatase 2C 16	B	321	Arabidopsis thaliana	Mutation(s): 0  Gene Names: HAB1, P2C-HA, At1g72770, F28P22.4 EC: 3.1.3.16
UniProt
Find proteins for Q9CAJ0 (Arabidopsis thaliana) Explore Q9CAJ0  Go to UniProtKB:  Q9CAJ0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A8S	C [auth A]	(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid C15 H20 O4 JLIDBLDQVAYHNE-YKALOCIXSA-N
MG	D [auth B], E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A8S	PDBBind:  3KB3	IC50: 150 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.259 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.319	α = 90
b = 67.466	β = 90
c = 143.905	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Zhou, X.E., Melcher, K., Soon, F.-F., Ng, L.-M., Xu, Y., Suino-Powell, K.M., Kovach, A., Li, J., Xu, H.E.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations, Structure summary