SAXSdb — 1bdg

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

HEXOKINASE

Schistosoma mansoni

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 1–451	Not recorded	GLC alpha-D-glucopyranose × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.60 Å R-free 0.256

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	HXK_SCHMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–451； UniProt 1–451

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	1bdg
Deposition date deposition_date	1998-05-08
Structure title title	HEXOKINASE FROM SCHISTOSOMA MANSONI COMPLEXED WITH GLUCOSE
Keywords keywords	HEXOKINASE, PHOSPHOTRANSFERASE; HEXOKINASE
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	23.37 Å
Radius of gyration Rg (electron density) rg_electron	22.40 Å
Forward intensity I(0) i0	39776300.00
Molecular weight molecular_weight	48200.0 kDa
Excluded volume excluded_volume	60019 Å³
Envelope volume envelope_volume	69878 Å³
Hydration-shell volume shell_volume	25798 Å³
Envelope diameter envelope_diameter	81.2 Å
Shell Rg shell_rg	29.74 Å
Envelope Rg envelope_rg	22.78 Å
Shape Rg shape_rg	22.43 Å
Total Rg total_rg	23.16 Å
Total atoms total_atoms	3377
Residues n_residues	444
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	78.7 Å
Rg (real space) rg_real	23.32 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	3.9780e+07
I(0) uncertainty (real space) i0_real_error	5.5740e+05
Rg (reciprocal space) rg_reciprocal	23.33 Å
I(0) (reciprocal space) i0_reciprocal	39780000.0000
Solution quality estimate total_estimate	0.8785
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.303
Kurtosis Kurtosis kurtosis	-0.358
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12950000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	HEXOKINASE
Molecular weight formula_weight	50510.9 kDa
EC 编号 ec_number	2.7.1.1
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	3481

MVFSDQQLFEKVVEILKPFDLSVVDYEEICDRMGESMRLGLQKSTNEKSSIKMFPSYVTKTPNGTETGNFLALDLGGTNYRVLSVTLEGKGKSPRIQERTYCIPAEKMSGSGTELFKYIAETLADFLENNGMKDKKFDLGFTFSFPCVQKGLTHATLVRWTKGFSADGVEGHNVAELLQTELDKRELNVKCVAVVNDTVGTLASCALEDPKCAVGLIVGTGTNVAYIEDSSKVELMDGVKEPEVVINTEWGAFGEKGELDCWRTQFDKSMDIDSLHPGKQLYEKMVSGMYLGELVRHIIVYLVEQKILFRGDLPERLKVRNSLLTRYLTDVERDPAHLLYNTHYMLTDDLHVPVVEPIDNRIVRYACEMVVKRAAYLAGAGIACILRRINRSEVTVGVDGSLYKFHPKFCERMTDMVDKLKPKNTRFCLRLSEDGSGKGAAAIAASCTRQN

来源 Source

来源生物 organism	Schistosoma mansoni
NCBI Class编号 ncbi_taxonomy_id	6183
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	alpha-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bdga1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

Domain ID domain_id	d1bdga2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

CATH v4.4 (2 domains)

Domain ID domain_id	1bdgA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1bdgA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

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8. Citations (1)

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Unit-cell length a length_a	114.300 Å
Unit-cell length b length_b	114.300 Å
Unit-cell length c length_c	155.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1730
R_work r_work	0.1730
R_free r_free	0.2560

fit	/app/data/saxs_computation/bd/1bdg/1bdg.fit
pddf	/app/data/pr_computation/bd/1bdg/1bdg.pr.out
profile	/app/data/saxs_computation/bd/1bdg/1bdg.dat

HEXOKINASE FROM SCHISTOSOMA MANSONI COMPLEXED WITH GLUCOSE

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

HEXOKINASE

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