SAXSdb — 5jfi

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

Leucine-rich repeat receptor-like protein kinase TDR

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CLE41 × 1 （A0A178VDH8） 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CLE41 × 1 （A0A178VDH8） 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TDR_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–613； UniProt 30–642 Author chain B； PDBConstruct 1–613； UniProt 30–642

CLE41

OrganismNot specified

UniProt A0A178VDH8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Leucine-rich repeat receptor-like protein kinase TDR × 1 （Q9FII5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Leucine-rich repeat receptor-like protein kinase TDR × 1 （Q9FII5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A178VDH8_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–12； UniProt 88–99 Author chain D； PDBConstruct 1–12； UniProt 88–99

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5jfi
Deposition date deposition_date	2016-04-19
Structure title title	Crystal structure of a TDIF-TDR complex
Keywords keywords	TDIF peptide, TDR receptor extracellular domain, LRR, glycosylation, hydroxylation, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

5jfi__assembly_1__model_1

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

Download this curve (.dat)

5jfi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jfi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.13 Å
Rg (electron density)	32.84 Å
Total Rg	33.40 Å
Atom count	4622
Residues	587
Excluded volume	82274 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jfi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5jfi__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Leucine-rich repeat receptor-like protein kinase TDR
Molecular weight formula_weight	67429.9 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9400

LKFSPQLLSLLSLKTSLSGPPSAFQDWKVPVNGQNDAVWCSWSGVVCDNVTAQVISLDLSHRNLSGRIPIQIRYLSSLLYLNLSGNSLEGSFPTSIFDLTKLTTLDISRNSFDSSFPPGISKLKFLKVFNAFSNNFEGLLPSDVSRLRFLEELNFGGSYFEGEIPAAYGGLQRLKFIHLAGNVLGGKLPPRLGLLTELQHMEIGYNHFNGNIPSEFALLSNLKYFDVSNCSLSGSLPQELGNLSNLETLFLFQNGFTGEIPESYSNLKSLKLLDFSSNQLSGSIPSGFSTLKNLTWLSLISNNLSGEVPEGIGELPELTTLFLWNNNFTGVLPHKLGSNGKLETMDVSNNSFTGTIPSSLCHGNKLYKLILFSNMFEGELPKSLTRCESLWRFRSQNNRLNGTIPIGFGSLRNLTFVDLSNNRFTDQIPADFATAPVLQYLNLSTNFFHRKLPENIWKAPNLQIFSASFSNLIGEIPNYVGCKSFYRIELQGNSLNGTIPWDIGHCEKLLCLNLSQNHLNGIIPWEISTLPSIADVDLSHNLLTGTIPSDFGSSKTITTFNVSYNQLIGPIPSGSFAHLNPSFFSSNEGLCGDLVGKPCNSDRFNAGNADIDG

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	Insect cell expression vector pTIE1

Entity 2 Entity 2 polymer

Description description	CLE41
Molecular weight formula_weight	1280.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

HEVPSGPNPISN

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	156

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Unit-cell length a length_a	92.445 Å
Unit-cell length b length_b	92.445 Å
Unit-cell length c length_c	252.615 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	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.749 Å
Low-resolution limit resolution_low	46.223 Å
R factor r_factor	0.2156
R_work r_work	0.2140
R_free r_free	0.2665

Crystal structure of a TDIF-TDR complex

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

Leucine-rich repeat receptor-like protein kinase TDR

State in the Current Structure

Other States of the Same Protein in the Database

CLE41

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

5jfi__assembly_1__model_1

5jfi__assembly_1__model_1 | I(q)

5jfi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of a TDIF-TDR complex

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

Leucine-rich repeat receptor-like protein kinase TDR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CLE41

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

5jfi__assembly_1__model_1

5jfi__assembly_1__model_1 | I(q)

5jfi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)