9q3h

GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC

Method: X-RAY DIFFRACTION

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

Platelet binding protein GspB

Streptococcus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 GLYCEROL × 2 Fluorenylmethyloxycarbonyl chloride × 2 SERINE × 2 CALCIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GSPB_STRGN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–127； UniProt 399–521 Author chain B； PDBConstruct 5–127； UniProt 399–521

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	9q3h
Deposition date deposition_date	2025-08-18
Last revision last_revision	2025-09-10
Structure title title	GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC
Keywords keywords	SLBR, SUGAR BINDING PROTEIN; SUGAR BINDING 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.

9q3h__assembly_1__model_1

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

Download this curve (.dat)

9q3h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9q3h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.55 Å
Rg (electron density)	18.70 Å
Total Rg	19.50 Å
Atom count	3942
Residues	247
Excluded volume	36711 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9q3h__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Platelet binding protein GspB
Molecular weight formula_weight	13952.4 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	4117

GPGSDTERPVVNVPSEITVYRGESFEYFATVTDNSNAFDLAKTVVRWLYSNQPGRGTEWLQYSVTQVGNQLKVRIFGNVPIDTTIGDYTRYVVATDAAGNVNATQTEMGNAAVDKTSVNGQFKLIIR

Source Source

Source organism organism	Streptococcus
NCBI taxonomy ID ncbi_taxonomy_id	1301
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose
Molecular weight formula_weight	674.6 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	Fluorenylmethyloxycarbonyl chloride
Molecular weight formula_weight	258.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SERINE
Molecular weight formula_weight	105.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	133

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Unit-cell length a length_a	37.987 Å
Unit-cell length b length_b	38.111 Å
Unit-cell length c length_c	47.054 Å
Unit-cell angle α angle_alpha	70.20 °
Unit-cell angle β angle_beta	68.01 °
Unit-cell angle γ angle_gamma	62.08 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	23.100 Å
R factor r_factor	0.1851
R_work r_work	0.1837
R_free r_free	0.2109

GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC

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

Platelet binding protein GspB

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

9q3h__assembly_1__model_1

9q3h__assembly_1__model_1 | I(q)

9q3h__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC

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

Platelet binding protein GspB

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

9q3h__assembly_1__model_1

9q3h__assembly_1__model_1 | I(q)

9q3h__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)