SAXSdb — 6t9e

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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 6	DutaFab mat VH chain × 2 DutaFab mat VL chain × 2	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	3
Chains and sequence ranges	Author chain CCC； PDBConstruct 1–109； UniProt 82–190 Author chain DDD； PDBConstruct 1–109； UniProt 82–190

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	6t9e
Deposition date deposition_date	2019-10-28
Structure title title	Crystal structure of a bispecific DutaFab in complex with human PDGF
Keywords keywords	monoclonal antibody, bispecific antibody, Fab fragment, PDGF, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

6t9e__assembly_1__model_1

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

Download this curve (.dat)

6t9e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6t9e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.38 Å
Rg (electron density)	42.12 Å
Total Rg	42.30 Å
Atom count	7935
Residues	1024
Excluded volume	140420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6t9e__assembly_1__model_1`	hexameric （6）	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	DutaFab mat VH chain
Molecular weight formula_weight	23502.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,HHH
Atom count atom_count	7935

DLQLVESGGGLVKPGGSLRLSCAADGWWFGYTDMSWVRQAPGKGLEWVGSISYKGGSTYYNTKFIGRFTISRDDDTNTLYLQMNSLRAEDTAVYYCARDDGYFDTWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYICNVNHKPSNTKVDKKVEPKSCT

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	DutaFab mat VL chain
Molecular weight formula_weight	23923.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	BBB,LLL

AIQMTQSPSSLSASVGDRVTITCHGSYWLSNYLAWYQQKPGKAPKLLIYDGKEREHGVPSRFSGSGSHEDYTLTISSLQPEDFATYYCQQYRYHPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 polymer

Description description	Platelet-derived growth factor subunit B
Molecular weight formula_weight	12313.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	CCC,DDD

SLGSLTIAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETVAAARPVT

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	89.301 Å
Unit-cell length b length_b	75.474 Å
Unit-cell length c length_c	116.505 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.989 Å
Low-resolution limit resolution_low	29.735 Å
R factor r_factor	—
R_work r_work	0.2531
R_free r_free	0.3044

Crystal structure of a bispecific DutaFab in complex with human PDGF

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6t9e__assembly_1__model_1

6t9e__assembly_1__model_1 | I(q)

6t9e__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)

Crystal structure of a bispecific DutaFab in complex with human PDGF

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6t9e__assembly_1__model_1

6t9e__assembly_1__model_1 | I(q)

6t9e__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)