SAXSdb — 9ezw

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

V-set and immunoglobulin domain-containing protein 4

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	single-domain antibody VHH_h3 × 1 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	single-domain antibody VHH_h3 × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	single-domain antibody VHH_h3 × 1 1,2-ETHANEDIOL × 3 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	single-domain antibody VHH_h3 × 1 1,2-ETHANEDIOL × 4 DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VSIG4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–118； UniProt 20–137 Author chain C； PDBConstruct 1–118； UniProt 20–137 Author chain E； PDBConstruct 1–118； UniProt 20–137 Author chain G； PDBConstruct 1–118； UniProt 20–137

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	9ezw
Deposition date deposition_date	2024-04-14
Structure title title	Structure of the single-domain antibody VHH_h3 in complex with human Vsig4
Keywords keywords	VHH, nanobody, in silico, antibody, complex, single-domain, 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.

9ezw__assembly_1__model_1

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

Download this curve (.dat)

9ezw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ezw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.50 Å
Rg (electron density)	19.79 Å
Total Rg	20.67 Å
Atom count	1916
Residues	243
Excluded volume	33619 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ezw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9ezw__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9ezw__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9ezw__assembly_4__model_1`	dimeric （2）	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	V-set and immunoglobulin domain-containing protein 4
Molecular weight formula_weight	14486.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	8368

RPILEVPESVTGPWKGDVNLPCTYDPLQGYTQVLVKWLVQRGSDPVTIFLRDSSGDHIQQAKYQGRLHVSHKVPGDVSLQLSTLEMDDRSHYTCEVTWQTPDGNQVVRDKITELRVQKAAAHHHHHH

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 2 Entity 2 polymer

Description description	single-domain antibody VHH_h3
Molecular weight formula_weight	14795.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

QVQLVESGGGLVQAGGSLRLSCAASGRTFSSYGMGWFRQAPGKEREFVAAIGPFGGTTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAGRWNRYGEQDQYNYEYWGQGTQVTVSSAAAHHHHHH

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	519

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Unit-cell length a length_a	60.867 Å
Unit-cell length b length_b	129.941 Å
Unit-cell length c length_c	144.284 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	16

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	64.970 Å
R factor r_factor	0.1942
R_work r_work	0.1904
R_free r_free	0.2280

Structure of the single-domain antibody VHH_h3 in complex with human Vsig4

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

V-set and immunoglobulin domain-containing protein 4

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

9ezw__assembly_1__model_1

9ezw__assembly_1__model_1 | I(q)

9ezw__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

7. Citations (1)

Structure of the single-domain antibody VHH_h3 in complex with human Vsig4

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

V-set and immunoglobulin domain-containing protein 4

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

9ezw__assembly_1__model_1

9ezw__assembly_1__model_1 | I(q)

9ezw__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

7. Citations (1)