SAXSdb — 6t9d

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

Vascular endothelial growth factor A

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	VP mat DutaFab VH chain × 2 VP mat DutaFab VL chain × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VEGFA_HUMAN
Isoform	P15692-9
PDB entities	3
Chains and sequence ranges	Author chain CCC； PDBConstruct 1–121； UniProt 27–147 Author chain DDD； PDBConstruct 1–121； UniProt 27–147

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	6t9d
Deposition date deposition_date	2019-10-28
Structure title title	Crystal structure of a bispecific DutaFab in complex with human VEGF121
Keywords keywords	monoclonal antibody, bispecific antibody, Fab fragment, VEGF, 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.

6t9d__assembly_1__model_1

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

Download this curve (.dat)

6t9d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6t9d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.36 Å
Rg (electron density)	32.73 Å
Total Rg	33.36 Å
Atom count	8047
Residues	1033
Excluded volume	142260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6t9d__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 (4)

Entity 1 Entity 1 polymer

Description description	VP mat DutaFab 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	8284

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	VP mat DutaFab VL chain
Molecular weight formula_weight	23820.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AIQMTQSPSSLSASVGDRVTITCHGSYWLSNYLAWYQQKPGKAPKLLIYDGKEREHGVPSRFSGSGSHEDYTLTISSLQPEDFATYYCQQYRYHPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

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	Vascular endothelial growth factor A
Molecular weight formula_weight	14078.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

APMAEGGGQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKDRARQENCDKPRR

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	213

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Unit-cell length a length_a	70.080 Å
Unit-cell length b length_b	107.875 Å
Unit-cell length c length_c	87.369 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.34 °
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	2.905 Å
Low-resolution limit resolution_low	29.294 Å
R factor r_factor	—
R_work r_work	0.2124
R_free r_free	0.2801

Crystal structure of a bispecific DutaFab in complex with human VEGF121

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

Vascular endothelial growth factor A

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

6t9d__assembly_1__model_1

6t9d__assembly_1__model_1 | I(q)

6t9d__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of a bispecific DutaFab in complex with human VEGF121

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

Vascular endothelial growth factor A

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

6t9d__assembly_1__model_1

6t9d__assembly_1__model_1 | I(q)

6t9d__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

7. Citations (1)