SAXSdb — 5dqq

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Two pore calcium channel protein 1

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 14 PALMITIC ACID × 2 trans-Ned 19 × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TPC1_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–723； UniProt 12–733

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5dqq
Deposition date deposition_date	2015-09-15
Structure title title	Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana
Keywords keywords	;membrane protein, ion channel, calcium channel, sodium channel, phosphorylation dependent ion channel, asymmetric ion channel, tandem pore-forming domains, EF-hand domain, N-terminal domain, C-terminal domain, calcium sensors, voltage sensor, selectivity filter, pore gate, TRANSPORT PROTEIN-INHIBITOR complex ;; TRANSPORT PROTEIN/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5dqq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5dqq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dqq__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	38.15 Å
Rg (electron density)	36.99 Å
Total Rg	37.53 Å
Atom count	10690
Residues	1298
Excluded volume	194810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dqq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Two pore calcium channel protein 1
Molecular weight formula_weight	83843.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5402

MGGGGTDRVRRSEAITHGTPFQKAAALVDLAEDGIGLPVEILDQSSFGESARYYFIFTRLDLIWSLNYFALLFLNFFEQPLWCEKNPKPSCKDRDYYYLGELPYLTNAESIIYEVITLAILLVHTFFPISYEGSRIFWTSRLNLVKVACVVILFVDVLVDFLYLSPLAFDFLPFRIAPYVRVIIFILSIRELRDTLVLLSGMLGTYLNILALWMLFLLFASWIAFVMFEDTQQGLTVFTSYGATLYQMFILFTTSNNPDVWIPAYKSSRWSSVFFVLYVLIGVYFVTNLILAVVYDSFKEQLAKQVSGMDQMKRRMLEKAFGLIDSDKNGEIDKNQCIKLFEQLTNYRTLPKISKEEFGLIFDELDDTRDFKINKDEFADLCQAIALRFQKEEVPSLFEHFPQIYHSALSQQLRAFVRSPNFGYAISFILIINFIAVVVETTLDIEESSAQKPWQVAEFVFGWIYVLEMALKIYTYGFENYWREGANRFDFLVTWVIVIGETATFITPDENTFFSNGEWIRYLLLARMLRLIRLLMNVQRYRAFIATFITLIPSLMPYLGTIFCVLCIYCSIGVQVFGGLVNAGNKKLFETELAEDDYLLFNFNDYPNGMVTLFNLLVMGNWQVWMESYKDLTGTWWSITYFVSFYVITILLLLNLVVAFVLEAFFTELDLEEEEKCQGQDSQEKRNRRRSAGSKSRSQRVDTLLHHMLGDELSKPECSTSDT

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	trans-Ned 19
Molecular weight formula_weight	514.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5dqqA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	350 — Voltage-gated potassium channels. Chain C

Domain ID domain_id	5dqqA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

▶

Unit-cell length a length_a	88.180 Å
Unit-cell length b length_b	154.810 Å
Unit-cell length c length_c	219.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.872 Å
Low-resolution limit resolution_low	38.703 Å
R factor r_factor	0.2990
R_work r_work	0.2970
R_free r_free	0.3394

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Two pore calcium channel protein 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5dqq__assembly_1__model_1

5dqq__assembly_1__model_1 | I(q)

5dqq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Two pore calcium channel protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5dqq__assembly_1__model_1

5dqq__assembly_1__model_1 | I(q)

5dqq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)