SAXSdb — 3mjg

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

Platelet-derived growth factor subunit B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Beta-type platelet-derived growth factor receptor × 2 （P09619） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Beta-type platelet-derived growth factor receptor × 2 （P09619） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDGFB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–165； UniProt 21–185 Author chain B； PDBConstruct 1–165； UniProt 21–185

Beta-type platelet-derived growth factor receptor

Homo sapiens

UniProt P09619

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Platelet-derived growth factor subunit B × 2 （P01127） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Platelet-derived growth factor subunit B × 2 （P01127） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PGFRB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain X； PDBConstruct 1–282； UniProt 33–314 Author chain Y； PDBConstruct 1–282； UniProt 33–314

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	3mjg
Deposition date deposition_date	2010-04-12
Structure title title	The structure of a platelet derived growth factor receptor complex
Keywords keywords	protein-protein complex, growth factor-receptor complex, Transferase-Hormone complex, Hormone-Transferase complex; Hormone/Transferase
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.

3mjg__assembly_1__model_1

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

Download this curve (.dat)

3mjg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3mjg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.69 Å
Rg (electron density)	39.84 Å
Total Rg	39.87 Å
Atom count	6084
Residues	745
Excluded volume	108440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3mjg__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3mjg__assembly_2__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	Platelet-derived growth factor subunit B
Molecular weight formula_weight	19596.3 kDa
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	7254

EGDPIPEELYEMLSDHSIRSFDDLQRLLHGDPGEEDGAELDLNMTRSHSGGELESLARGRRSLGSLTIAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETVAAHHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Beta-type platelet-derived growth factor receptor
Molecular weight formula_weight	32493.4 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y

LVVTPPGPELVLNVSSTFVLTCSGSAPVVWERMSQEPPQEMAKAQDGTFSSVLTLTNLTGLDTGEYFCTHNDSRGLETDERKRLYIFVPDPTVGFLPNDAEELFIFLTEITEITIPCRVTDPQLVVTLHEKKGDVALPVPYDHQRGFSGIFEDRSYICKTTIGDREVDSDAYYVYRLQVSSINVSVNAVQTVVRQGENITLMCIVIGNEVVNFEWTYPRKESGRLVEPVTDFLLDMPYHIRSILHIPSAELEDSGTYTCNVTESVNDHQDEKAINITVVESGHHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-alpha-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 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	13

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1170

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3mjga_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

Domain ID domain_id	d3mjgb_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

CATH v4.4 (8 domains)

Domain ID domain_id	3mjgA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	3mjgB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	3mjgX01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3mjgX02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3mjgX03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3mjgY01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3mjgY02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3mjgY03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	78.470 Å
Unit-cell length b length_b	116.820 Å
Unit-cell length c length_c	134.150 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	44.240 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2770

The structure of a platelet derived growth factor receptor complex

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

Platelet-derived growth factor subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Beta-type platelet-derived growth factor receptor

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

3mjg__assembly_1__model_1

3mjg__assembly_1__model_1 | I(q)

3mjg__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)

The structure of a platelet derived growth factor receptor complex

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

Platelet-derived growth factor subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-type platelet-derived growth factor receptor

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

3mjg__assembly_1__model_1

3mjg__assembly_1__model_1 | I(q)

3mjg__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)