6NWB | pdb_00006nwb

PYL10 bound to the selective agonist hexabactin

PDB DOI: https://doi.org/10.2210/pdb6NWB/pdb

Classification: PLANT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-02-06 Released: 2020-02-12
Deposition Author(s): Peterson, F.C., Vaidya, A., Jensen, D.R., Volkman, B.F., Cutler, S.R.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.224 (Depositor), 0.227 (DCC)
R-Value Work:
0.174 (Depositor), 0.175 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

PYL10 bound to the selective agonist hexabactin

Elzinga, D., Vaidya, A.S., Peterson, F.C., Park, S.Y., Volkman, B.F., Okamoto, M., Cutler, S.R.

To be published.

Macromolecule Content

Total Structure Weight: 17.76 kDa
Atom Count: 1,346
Modeled Residue Count: 156
Deposited Residue Count: 156
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Abscisic acid receptor PYL10	A	156	Arabidopsis thaliana	Mutation(s): 0 Gene Names: PYL10, RCAR4, At4g27920, T13J8.30
UniProt
Find proteins for Q8H1R0 (Arabidopsis thaliana) Explore Q8H1R0 Go to UniProtKB: Q8H1R0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8H1R0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L6V Query on L6V Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-{[(4-cyanophenyl)methyl]sulfonyl}-1-(thiophen-3-yl)cyclohexane-1-carboxamide C₁₉ H₂₀ N₂ O₃ S₂ KAEXAGMLFGNNER-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224 (Depositor), 0.227 (DCC)
R-Value Work: 0.174 (Depositor), 0.175 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.91	α = 90
b = 65.91	β = 90
c = 65.03	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	12581750
National Science Foundation (NSF, United States)	United States	165689

Revision History (Full details and data files)

Version 1.0: 2020-02-12
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.