5t05

Crystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and IdoA2S containing hexasaccharide substrate

Method: X-RAY DIFFRACTION

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

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein

Danio rerio

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 其他Polymer 2	;2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 ADENOSINE-3'-5'-DIPHOSPHATE × 1 P-NITROPHENOL × 1 1,2-ETHANEDIOL × 9 CHLORIDE ION × 3 SODIUM ION × 5 L(+)-TARTARIC ACID × 2 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1 其他Polymer 2	;2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 ADENOSINE-3'-5'-DIPHOSPHATE × 1 P-NITROPHENOL × 1 1,2-ETHANEDIOL × 6 CHLORIDE ION × 1 SODIUM ION × 2 L(+)-TARTARIC ACID × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H6ST3_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 372–692； UniProt 75–395 Author chain B； PDBConstruct 372–692； UniProt 75–395

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein

Danio rerio

UniProt P0AEY0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 其他Polymer 2	;2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 ADENOSINE-3'-5'-DIPHOSPHATE × 1 P-NITROPHENOL × 1 1,2-ETHANEDIOL × 9 CHLORIDE ION × 3 SODIUM ION × 5 L(+)-TARTARIC ACID × 2 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1 其他Polymer 2	;2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 ADENOSINE-3'-5'-DIPHOSPHATE × 1 P-NITROPHENOL × 1 1,2-ETHANEDIOL × 6 CHLORIDE ION × 1 SODIUM ION × 2 L(+)-TARTARIC ACID × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–367； UniProt 27–392 Author chain B； PDBConstruct 2–367； UniProt 27–392

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	5t05
Deposition date deposition_date	2016-08-15
Structure title title	Crystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and IdoA2S containing hexasaccharide substrate
Keywords keywords	heparan sulfate, sulfotransferase, complex, TRANSFERASE; 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.

5t05__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5t05__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5t05__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.41 Å
Rg (electron density)	30.63 Å
Total Rg	31.28 Å
Atom count	5472
Residues	677
Excluded volume	96828 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5t05__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5t05__assembly_2__model_1`	monomeric （1）	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 (10)

Entity 1 Entity 1 polymer

Description description	maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
Molecular weight formula_weight	78557.2 kDa
EC 编号 ec_number	2.8.2.-
Mutation mutation	D82A, K83A, E172A, N173A, K239A, E359A, K362A, D363A
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	12096

MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAKFNFTERDLTRDVDFNIKGDDVIVFLHIQKTGGTTFGRHLVRNIRLEQPCDCKAGQKKCTCHRPGKQESWLFSRFSTGWSCGLHADWTELTNCVPVIMDKRQPPKRKRNFYYITMLRDPVSRYLSEWKHVQRGATWKTSLHMCDGRSPTQDELPTCYNGDDWSGVTLHDFMDCPSNLANNRQVRMLADLSLVGCYNLSTMNESERNPILLASAKSNLKNMAFYGLTEFQRKTQYLFERTFHLRFISAFTQINSTRAANVELRDDMRSRIEQLNMLDMQLYEFAKDLFLQRYQFVRQRERQEERLKRREERRWIRERRVNQS

Source Source

Source organism organism	Danio rerio
Common name common_name	Zebrafish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	;2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ;
Molecular weight formula_weight	1350.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	666.6 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-3'-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	P-NITROPHENOL
Molecular weight formula_weight	139.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	man
Copy count entity_count	15

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	man
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	man
Copy count entity_count	7

Entity 9 Entity 9 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	4

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1067

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5t05A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5t05B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	75.785 Å
Unit-cell length b length_b	128.161 Å
Unit-cell length c length_c	178.711 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	1.952 Å
Low-resolution limit resolution_low	38.487 Å
R factor r_factor	0.1786
R_work r_work	0.1779
R_free r_free	0.2120

Crystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and IdoA2S containing hexasaccharide substrate

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

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein

State in the Current Structure

Other States of the Same Protein in the Database

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein

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

5t05__assembly_2__model_1

5t05__assembly_2__model_1 | I(q)

5t05__assembly_2__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and IdoA2S containing hexasaccharide substrate

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

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein

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

5t05__assembly_2__model_1

5t05__assembly_2__model_1 | I(q)

5t05__assembly_2__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)