3KB3 | pdb_00003kb3

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.259 (Depositor), 0.263 (DCC)
R-Value Work:
0.214 (Depositor), 0.218 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O80992
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CAJ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A8S Query on A8S Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	D [auth B], E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.259 (Depositor), 0.263 (DCC)
R-Value Work: 0.214 (Depositor), 0.218 (DCC)
R-Value Observed: 0.217 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-12-08

Deposition Author(s):

Revision History (Full details and data files)

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