SAXSdb — 5sax

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

Epithelial discoidin domain-containing receptor 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	IODIDE ION × 8 2-{3-[(pyridin-3-yl)ethynyl]phenyl}-N-[3-(trifluoromethyl)phenyl]acetamide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–315； UniProt 593–913

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	5sax
Deposition date deposition_date	2021-06-22
Structure title title	DDR1, 2-[3-(2-pyridin-3-ylethynyl)phenyl]-N-[3-(trifluoromethyl)phenyl]acetamide, 1.902A, second P212121 form, Rfree=25.4%, second form
Keywords keywords	RTK, RECEPTOR TYROSINE KINASE, COLLAGEN, DISCOIDIN DOMAIN;, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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.

5sax__assembly_1__model_1

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

Download this curve (.dat)

5sax__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5sax__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.38 Å
Rg (electron density)	20.35 Å
Total Rg	21.16 Å
Atom count	2450
Residues	302
Excluded volume	43742 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5sax__assembly_1__model_1`	monomeric （1）	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	Epithelial discoidin domain-containing receptor 1
Molecular weight formula_weight	36502.9 kDa
EC 编号 ec_number	2.7.10.1
Mutation mutation	Deletion of residues 730-735
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	2600

PGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTVHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	2-{3-[(pyridin-3-yl)ethynyl]phenyl}-N-[3-(trifluoromethyl)phenyl]acetamide
Molecular weight formula_weight	380.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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Unit-cell length a length_a	62.250 Å
Unit-cell length b length_b	73.760 Å
Unit-cell length c length_c	74.310 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.902 Å
Low-resolution limit resolution_low	40.065 Å
R factor r_factor	0.2118
R_work r_work	0.2094
R_free r_free	0.2544

DDR1, 2-[3-(2-pyridin-3-ylethynyl)phenyl]-N-[3-(trifluoromethyl)phenyl]acetamide, 1.902A, second P212121 form, Rfree=25.4%, second form

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

Epithelial discoidin domain-containing receptor 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

5sax__assembly_1__model_1

5sax__assembly_1__model_1 | I(q)

5sax__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

DDR1, 2-[3-(2-pyridin-3-ylethynyl)phenyl]-N-[3-(trifluoromethyl)phenyl]acetamide, 1.902A, second P212121 form, Rfree=25.4%, second form

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

Epithelial discoidin domain-containing receptor 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

5sax__assembly_1__model_1

5sax__assembly_1__model_1 | I(q)

5sax__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)