SAXSdb — 7aym

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

Discoidin domain-containing receptor 2,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	Insufficient information	Monomer	Protein 1	N-[5-({[(3-fluorophenyl)carbamoyl]amino}methyl)-2-methylphenyl]imidazo[1,2-a]pyridine-3-carboxamide × 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 141–160； UniProt 717–736 Author chain A； PDBConstruct 330–337； UniProt 906–913

Discoidin domain-containing receptor 2,Epithelial discoidin domain-containing receptor 1

Homo sapiens

UniProt Q16832

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	N-[5-({[(3-fluorophenyl)carbamoyl]amino}methyl)-2-methylphenyl]imidazo[1,2-a]pyridine-3-carboxamide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDR2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 29–140； UniProt 558–669 Author chain A； PDBConstruct 161–329； UniProt 681–849

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	7aym
Deposition date deposition_date	2020-11-12
Structure title title	Structure of DDR2 Kinase domain in complex with IBZ3
Keywords keywords	;Kinase, Receptor Tyrosine kinase Discoidin domain-containing receptor 2, collagen, signal transduction, cell communication, MEMBRANE PROTEIN ;; MEMBRANE 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.

7aym__assembly_1__model_1

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

Download this curve (.dat)

7aym__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7aym__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.68 Å
Rg (electron density)	19.65 Å
Total Rg	20.65 Å
Atom count	2280
Residues	275
Excluded volume	40298 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7aym__assembly_1__model_1`	monomer （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 (3)

Entity 1 Entity 1 polymer

Description description	Discoidin domain-containing receptor 2,Epithelial discoidin domain-containing receptor 1
Molecular weight formula_weight	38627.8 kDa
EC 编号 ec_number	2.7.10.1
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	2293

MGSSHHHHHHDYDIPTTENLYFQGPRVDFPRKLLTFKEKLGEGQFGEVHLCEVEGMEKFKDKDFALDVSANQPVLVAVKMLRADANKNARNDFLKEIKIMSRLKDPNIIHLLAVCITDDPLCMITEYMENGDLNQFLSRHQLEDKAAEGAPGDGQAAQGPTVSYTNLKFMATQIASGMKYLSSLNFVHRDLATRNCLVGKNYTIKIADFGMSRNLYSGDYYRIQGRAVLPIRWMSWESILLGKFTTASDVWAFGVTLWETFTFCQEQPYSQLSDEQVIENTGEFFRDQGRQTYLPQPAICPDSVYELMLSCWRRDTKNRPSFQEIHRLLAEDALNTV

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	N-[5-({[(3-fluorophenyl)carbamoyl]amino}methyl)-2-methylphenyl]imidazo[1,2-a]pyridine-3-carboxamide
Molecular weight formula_weight	417.4 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d7ayma1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d7ayma2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	7aymA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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Unit-cell length a length_a	41.750 Å
Unit-cell length b length_b	85.355 Å
Unit-cell length c length_c	89.541 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	2.120 Å
Low-resolution limit resolution_low	61.780 Å
R factor r_factor	0.2390
R_work r_work	0.2360
R_free r_free	0.2890

Structure of DDR2 Kinase domain in complex with IBZ3

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

Discoidin domain-containing receptor 2,Epithelial discoidin domain-containing receptor 1

State in the Current Structure

Other States of the Same Protein in the Database

Discoidin domain-containing receptor 2,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

7aym__assembly_1__model_1

7aym__assembly_1__model_1 | I(q)

7aym__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of DDR2 Kinase domain in complex with IBZ3

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

Discoidin domain-containing receptor 2,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

Discoidin domain-containing receptor 2,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

7aym__assembly_1__model_1

7aym__assembly_1__model_1 | I(q)

7aym__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)