SAXSdb — 5l0u

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

Protein O-glucosyltransferase 1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 29–385	Not recorded	EGF(+) × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 660 [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG5000 MME, 50 mM MES pH 6.5, 10mM CaCl2, 250mM NaCl, 5% MPD	Resolution 1.80 Å R-free 0.194

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 5L0U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5L0R human POGLUT1 in complex with Notch1 EGF12 and UDP Deposited 2016-07-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–385（357 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% glycerol	Resolution 1.50 Å R-free 0.171
5L0S human POGLUT1 in complex with Factor VII EGF1 and UDP Deposited 2016-07-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–385（357 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 UDP URIDINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% glycerol	Resolution 1.45 Å R-free 0.159
5L0T human POGLUT1 in complex with EGF(+) and UDP Deposited 2016-07-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–385（357 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 UDP URIDINE-5'-DIPHOSPHATE × 1 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG5000 MME, 50 mM MES pH 6.5, 10mM CaCl2, 250mM NaCl, 5% glycerol	Resolution 1.43 Å R-free 0.173
5L0V human POGLUT1 in complex with 2F-glucose modified EGF(+) and UDP Deposited 2016-07-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–385（357 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 UDP URIDINE-5'-DIPHOSPHATE × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CA CALCIUM ION × 1 SHG 2-deoxy-2-fluoro-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG5000 MME, 50 mM MES pH 6.5, 10mM CaCl2, 250mM NaCl, 5% MPD	Resolution 1.30 Å R-free 0.174
5UB5 human POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP Deposited 2016-12-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–385（357 aa） Fragment：UNP residues 29-385	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 UDP URIDINE-5'-DIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% (v/v) PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% (v/v) 2-methyl-2,4-pentanediol	Resolution 2.09 Å R-free 0.193

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PGLT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–357； UniProt 29–385

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	5l0u
Deposition date deposition_date	2016-07-28
Structure title title	human POGLUT1 in complex with EGF(+) and UDP-phosphono-glucose
Keywords keywords	transferase glycosyltransferase GT-B glucosyltransferase, 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	22.58 Å
Radius of gyration Rg (electron density) rg_electron	21.65 Å
Forward intensity I(0) i0	37894200.00
Molecular weight molecular_weight	47170.0 kDa
Excluded volume excluded_volume	58780 Å³
Envelope volume envelope_volume	67997 Å³
Hydration-shell volume shell_volume	25696 Å³
Envelope diameter envelope_diameter	74.3 Å
Shell Rg shell_rg	29.00 Å
Envelope Rg envelope_rg	22.04 Å
Shape Rg shape_rg	21.61 Å
Total Rg total_rg	22.67 Å
Total atoms total_atoms	6460
Residues n_residues	396
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	73.4 Å
Rg (real space) rg_real	22.50 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	3.7890e+07
I(0) uncertainty (real space) i0_real_error	4.7450e+05
Rg (reciprocal space) rg_reciprocal	22.52 Å
I(0) (reciprocal space) i0_reciprocal	37890000.0000
Solution quality estimate total_estimate	0.6882
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.254
Kurtosis Kurtosis kurtosis	-0.326
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7084000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 0.130; Positv: 1.000; Valcen: 0.997; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Protein O-glucosyltransferase 1
Molecular weight formula_weight	42077.1 kDa
EC 编号 ec_number	2.4.1.-,2.4.2.26
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	6829

GSKWKVFIDQINRSLENYEPCSSQNCSCYHGVIEEDLTPFRGGISRKMMAEVVRRKLGTHYQITKNRLYRENDCMFPSRCSGVEHFILEVIGRLPDMEMVINVRDYPQVPKWMEPAIPVFSFSKTSEYHDIMYPAWTFWEGGPAVWPIYPTGLGRWDLFREDLVRSAAQWPWKKKNSTAYFRGSRTSPERDPLILLSRKNPKLVDAEYTKNQAWKSMKDTLGKPAAKDVHLVDHCKYKYLFNFRGVAASFRFKHLFLCGSLVFHVGDEWLEFFYPQLKPWVHYIPVKTDLSNVQELLQFVKANDDVAQEIAERGSQFIRNHLQMDDITCYWENLLSEYSKFLSYNVTRRKGYDQIIP

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	EGF(+)
Molecular weight formula_weight	4255.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSDIDECASNPCQNGGTCVNTVGSYTCLCPPGFTGPNCEDDI

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	;[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid ;
Molecular weight formula_weight	564.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	308

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5l0uB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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8. Citations (1)

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Unit-cell length a length_a	71.850 Å
Unit-cell length b length_b	74.390 Å
Unit-cell length c length_c	83.310 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	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	37.195 Å
R factor r_factor	0.1728
R_work r_work	0.1718
R_free r_free	0.1942

fit	/app/data/saxs_computation/l0/5l0u/5l0u.fit
pddf	/app/data/pr_computation/l0/5l0u/5l0u.pr.out
profile	/app/data/saxs_computation/l0/5l0u/5l0u.dat

human POGLUT1 in complex with EGF(+) and UDP-phosphono-glucose

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

Protein O-glucosyltransferase 1

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

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)