SAXSdb — 3bd9

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

Heparan sulfate glucosamine 3-O-sulfotransferase 5

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 88–346	Mutation：I299E	A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；100 mM sodium citrate pH 5.6, 35% (v/v) t-butanol, 4mM PAP, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.30 Å R-free 0.249

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3BD9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SCD Ternary complex of fixed-arm Trx-3ost5 (I299E) with 8mer-1 octasaccharide substrate and co-factor product PAP Deposited 2021-09-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 86–346（261 aa）	Mutation：I299E	A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium tartrate, 20% (w/v) PEG3350	Resolution 2.90 Å R-free 0.252
7SCE Ternary complex of fixed-arm Trx-3ost5 (I299E) with 8mer-2 octasaccharide substrate and co-factor product PAP Deposited 2021-09-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 86–346（261 aa）	Mutation：I299E	A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；295 K；85mM sodium acetate pH 4.6, 0.17M ammonium acetate, 25.5% (w/v) PEG4000, 15% (v/v) ethylene glycol	Resolution 2.75 Å R-free 0.246

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OST5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–280； UniProt 88–346

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	3bd9
Deposition date deposition_date	2007-11-14
Structure title title	human 3-O-sulfotransferase isoform 5 with bound PAP
Keywords keywords	;3-O-sulfotransferase, heparan sulfate, heparan sulfate biosynthesis, substrate specificity, Glycoprotein, Golgi apparatus, Membrane, Signal-anchor, Transmembrane, TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.08 Å
Radius of gyration Rg (electron density) rg_electron	19.01 Å
Forward intensity I(0) i0	14699500.00
Molecular weight molecular_weight	29910.0 kDa
Excluded volume excluded_volume	37859 Å³
Envelope volume envelope_volume	43492 Å³
Hydration-shell volume shell_volume	19225 Å³
Envelope diameter envelope_diameter	67.4 Å
Shell Rg shell_rg	25.17 Å
Envelope Rg envelope_rg	19.29 Å
Shape Rg shape_rg	18.99 Å
Total Rg total_rg	19.95 Å
Total atoms total_atoms	2115
Residues n_residues	258
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.3 Å
Rg (real space) rg_real	19.99 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.4700e+07
I(0) uncertainty (real space) i0_real_error	1.7240e+05
Rg (reciprocal space) rg_reciprocal	20.00 Å
I(0) (reciprocal space) i0_reciprocal	14700000.0000
Solution quality estimate total_estimate	0.8931
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.195
Kurtosis Kurtosis kurtosis	-0.367
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2420000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Heparan sulfate glucosamine 3-O-sulfotransferase 5
Molecular weight formula_weight	32969.0 kDa
EC 编号 ec_number	2.8.2.23
Mutation mutation	I299E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2202

MGSSHHHHHHSSGLVPRGSHMQQLPKAIIIGVRKGGTRALLEMLNLHPAVVKASQEIHFFDNDENYGKGIEWYRKKMPFSYPQQITIEKSPAYFITEEVPERIYKMNSSIKLLIIVREPTTRAISDYTQVLEGKERKNKTYYKFEKLAIDPNTCEVNTKYKAVRTSIYTKHLERWLKYFPIEQFHVVDGDRLITEPLPELQLVEKFLNLPPRISQYNLYFNATRGFYCLRFNEIFNKCLAGSKGRIHPEVDPSVITKLRKFFHPFNQKFYQITGRTLNWP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-3'-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3bd9a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d3bd9a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	3bd9A00
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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8. Citations (1)

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Unit-cell length a length_a	59.270 Å
Unit-cell length b length_b	59.270 Å
Unit-cell length c length_c	173.957 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	48.980 Å
R factor r_factor	0.2050
R_work r_work	0.2030
R_free r_free	0.2490

fit	/app/data/saxs_computation/bd/3bd9/3bd9.fit
pddf	/app/data/pr_computation/bd/3bd9/3bd9.pr.out
profile	/app/data/saxs_computation/bd/3bd9/3bd9.dat

human 3-O-sulfotransferase isoform 5 with bound PAP

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

Heparan sulfate glucosamine 3-O-sulfotransferase 5

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction