5DQQ

Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb5DQQ/pdb

Classification: TRANSPORT PROTEIN/INHIBITOR
Organism(s): Arabidopsis thaliana
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2015-09-15 Released: 2016-03-09
Deposition Author(s): Kintzer, A.F., Stroud, R.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free:
0.339 (Depositor), 0.340 (DCC)
R-Value Work:
0.297 (Depositor), 0.300 (DCC)
R-Value Observed:
0.299 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana

Kintzer, A.F., Stroud, R.M.

(2016) Nature 531: 258-262

Macromolecule Content

Total Structure Weight: 84.9 kDa
Atom Count: 5,402
Modelled Residue Count: 649
Deposited Residue Count: 723
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Two pore calcium channel protein 1	A	723	Arabidopsis thaliana	Mutation(s): 0 Gene Names: TPC1, CCH1, FOU2, At4g03560, F9H3.19, T5L23.5 Membrane Entity: Yes
UniProt
Find proteins for Q94KI8 (Arabidopsis thaliana) Explore Q94KI8 Go to UniProtKB: Q94KI8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q94KI8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
66R Query on 66R Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	trans-Ned 19 C₃₀ H₃₁ F N₄ O₃ FUHCEERDBRGPQZ-LBNVMWSVSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain B [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free: 0.339 (Depositor), 0.340 (DCC)
R-Value Work: 0.297 (Depositor), 0.300 (DCC)
R-Value Observed: 0.299 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.18	α = 90
b = 154.81	β = 90
c = 219.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHARP	phasing
DM	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Kintzer, A.F.

Stroud, R.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM24485

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2016-03-16
Changes: Database references
Version 1.2: 2017-09-13
Changes: Author supporting evidence, Database references, Derived calculations
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 1.4: 2024-03-06
Changes: Data collection, Database references, Derived calculations, Structure summary